Science.gov

Sample records for radiat prot dosim

  1. UniProtKB/Swiss-Prot.

    PubMed

    Boutet, Emmanuel; Lieberherr, Damien; Tognolli, Michael; Schneider, Michel; Bairoch, Amos

    2007-01-01

    The Swiss Institute of Bioinformatics (SIB), the European Bioinformatics Institute (EBI), and the Protein Information Resource (PIR) form the Universal Protein Resource (UniProt) consortium. Its main goal is to provide the scientific community with a central resource for protein sequences and functional information. The UniProt consortium maintains the UniProt KnowledgeBase (UniProtKB) and several supplementary databases including the UniProt Reference Clusters (UniRef) and the UniProt Archive (UniParc). (1) UniProtKB is a comprehensive protein sequence knowledgebase that consists of two sections: UniProtKB/Swiss-Prot, which contains manually annotated entries, and UniProtKB/TrEMBL, which contains computer-annotated entries. UniProtKB/Swiss-Prot entries contain information curated by biologists and provide users with cross-links to about 100 external databases and with access to additional information or tools. (2) The UniRef databases (UniRef100, UniRef90, and UniRef50) define clusters of protein sequences that share 100, 90, or 50% identity. (3) The UniParc database stores and maps all publicly available protein sequence data, including obsolete data excluded from UniProtKB. The UniProt databases can be accessed online (http://www.uniprot.org/) or downloaded in several formats (ftp://ftp.uniprot.org/pub). New releases are published every 2 weeks. The purpose of this chapter is to present a guided tour of a UniProtKB/Swiss-Prot entry, paying particular attention to the specificities of plant protein annotation. We will also present some of the tools and databases that are linked to each entry. PMID:18287689

  2. UniProt Tools.

    PubMed

    Pundir, Sangya; Martin, Maria J; O'Donovan, Claire

    2016-01-01

    The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data (UniProt Consortium, 2015). The UniProt Web site receives ∼400,000 unique visitors per month and is the primary means to access UniProt. Along with various datasets that you can search, UniProt provides three main tools. These are the 'BLAST' tool for sequence similarity searching, the 'Align' tool for multiple sequence alignment, and the 'Retrieve/ID Mapping' tool for using a list of identifiers to retrieve UniProtKB proteins and to convert database identifiers from UniProt to external databases or vice versa. This unit provides three basic protocols, three alternate protocols, and two support protocols for using UniProt tools. © 2016 by John Wiley & Sons, Inc. PMID:27010333

  3. Dose measurements in pulsed radiation fields with commercially available measuring components.

    PubMed

    Friedrich, Sabrina; Hupe, Oliver

    2016-03-01

    Dose measurements in pulsed radiation fields with dosemeters using the counting technique are known to be inappropriate. Therefore, there is a demand for a portable device able to measure the dose in pulsed radiation fields. As a detector, ionisation chambers seem to be a good alternative. In particular, using a secondary standard ionisation chamber in combination with a reliable charge-measuring system would be a good solution. The Physikalisch-Technische Bundesanstalt (PTB) uses secondary standard ionisation chambers in combination with PTB-made measuring electronics for dose measurements at its reference fields. However, for general use, this equipment is too complex. For measurements on-site, a mobile special electronic system [Hupe, O. and Ankerhold, U. Determination of ambient and personal dose equivalent for personnel and cargo security screening. Radiat. Prot. Dosim. 121: (4), 429-437 (2006)] has been used successfully. Still, for general use, there is a need for a much simpler but a just as good solution. A measuring instrument with very good energy dependence for H*(10) is the secondary standard ionisation chamber HS01. An easy-to-use and commercially available electrometer for measuring the generated charges is the UNIDOS by PTW Freiburg. Depending on the expected dose values, the ionisation chamber used can be selected. In addition, measurements have been performed by using commercially available area dosemeters, e.g. the Mini SmartION 2120S by Thermo Scientific, using an ionisation chamber and the Szintomat 6134 A/H by Automess, using a scintillation detector. PMID:26056377

  4. The Universal Protein Resource (UniProt)

    PubMed Central

    2008-01-01

    The Universal Protein Resource (UniProt) provides a stable, comprehensive, freely accessible, central resource on protein sequences and functional annotation. The UniProt Consortium is a collaboration between the European Bioinformatics Institute (EBI), the Protein Information Resource (PIR) and the Swiss Institute of Bioinformatics (SIB). The core activities include manual curation of protein sequences assisted by computational analysis, sequence archiving, development of a user-friendly UniProt website, and the provision of additional value-added information through cross-references to other databases. UniProt is comprised of four major components, each optimized for different uses: the UniProt Knowledgebase, the UniProt Reference Clusters, the UniProt Archive and the UniProt Metagenomic and Environmental Sequences database. UniProt is updated and distributed every three weeks, and can be accessed online for searches or download at http://www.uniprot.org. PMID:18045787

  5. The Universal Protein Resource (UniProt).

    PubMed

    Bairoch, Amos; Apweiler, Rolf; Wu, Cathy H; Barker, Winona C; Boeckmann, Brigitte; Ferro, Serenella; Gasteiger, Elisabeth; Huang, Hongzhan; Lopez, Rodrigo; Magrane, Michele; Martin, Maria J; Natale, Darren A; O'Donovan, Claire; Redaschi, Nicole; Yeh, Lai-Su L

    2005-01-01

    The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. Formed by uniting the Swiss-Prot, TrEMBL and PIR protein database activities, the UniProt consortium produces three layers of protein sequence databases: the UniProt Archive (UniParc), the UniProt Knowledgebase (UniProt) and the UniProt Reference (UniRef) databases. The UniProt Knowledgebase is a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase with extensive cross-references. This centrepiece consists of two sections: UniProt/Swiss-Prot, with fully, manually curated entries; and UniProt/TrEMBL, enriched with automated classification and annotation. During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; we introduced a new comment line topic: TOXIC DOSE to store information on the acute toxicity of a toxin; the UniProt keyword list got augmented by additional keywords; we improved the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications. Furthermore, we introduced a new documentation file of the strains and their synonyms. Many new database cross-references were introduced and we started to make use of Digital Object Identifiers. We also achieved in collaboration with the Macromolecular Structure Database group at EBI an improved integration with structural databases by residue level mapping of sequences from the Protein Data Bank entries onto corresponding UniProt entries. For convenient sequence searches we provide the UniRef non-redundant sequence databases. The comprehensive UniParc database stores the complete body of publicly available protein sequence data. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). New releases are published every two

  6. The Universal Protein Resource (UniProt)

    PubMed Central

    Bairoch, Amos; Apweiler, Rolf; Wu, Cathy H.; Barker, Winona C.; Boeckmann, Brigitte; Ferro, Serenella; Gasteiger, Elisabeth; Huang, Hongzhan; Lopez, Rodrigo; Magrane, Michele; Martin, Maria J.; Natale, Darren A.; O'Donovan, Claire; Redaschi, Nicole; Yeh, Lai-Su L.

    2005-01-01

    The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. Formed by uniting the Swiss-Prot, TrEMBL and PIR protein database activities, the UniProt consortium produces three layers of protein sequence databases: the UniProt Archive (UniParc), the UniProt Knowledgebase (UniProt) and the UniProt Reference (UniRef) databases. The UniProt Knowledgebase is a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase with extensive cross-references. This centrepiece consists of two sections: UniProt/Swiss-Prot, with fully, manually curated entries; and UniProt/TrEMBL, enriched with automated classification and annotation. During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; we introduced a new comment line topic: TOXIC DOSE to store information on the acute toxicity of a toxin; the UniProt keyword list got augmented by additional keywords; we improved the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications. Furthermore, we introduced a new documentation file of the strains and their synonyms. Many new database cross-references were introduced and we started to make use of Digital Object Identifiers. We also achieved in collaboration with the Macromolecular Structure Database group at EBI an improved integration with structural databases by residue level mapping of sequences from the Protein Data Bank entries onto corresponding UniProt entries. For convenient sequence searches we provide the UniRef non-redundant sequence databases. The comprehensive UniParc database stores the complete body of publicly available protein sequence data. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). New releases are published every two

  7. Track structure based modelling of light ion radiation effects on nuclear and mitochondrial DNA

    NASA Astrophysics Data System (ADS)

    Schmitt, Elke; Ottolenghi, Andrea; Dingfelder, Michael; Friedland, Werner; Kundrat, Pavel; Baiocco, Giorgio

    2016-07-01

    double-strand breaks", Mutat. Res. 793, 30-40 [4] Friedland, Schmitt, Kundrat (2015): "Modelling Proton bunches focussed to submicrometre scales: Low-LET Radiation damage in high-LET-like spatial structure", Radiat. Prot. Dosim. 166, 34-37 [5] Schmitt, Friedland, Kundrat, Dingfelder, Ottolenghi (2015): "Cross section scaling for track structure simulations of low-energy ions in liquid water", Radiat. Prot. Dosim. 166, 15-18} Supported by the European Atomic Energy Community's Seventh Framework Programme (FP7/2007-2011) under grant agreement no 249689 "DoReMi" and the German Federal Ministry on Education and Research (KVSF-Projekt "LET-Verbund").

  8. The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program

    PubMed Central

    Schneider, Michel; Lane, Lydie; Boutet, Emmanuel; Lieberherr, Damien; Tognolli, Michael; Bougueleret, Lydie; Bairoch, Amos

    2009-01-01

    The UniProt knowledgebase, UniProtKB, is the main product of the UniProt consortium. It consists of two sections, UniProtKB/Swiss-Prot, the manually curated section, and UniProtKB/TrEMBL, the computer translation of the EMBL/GenBank/DDBJ nucleotide sequence database. Taken together, these two sections cover all the proteins characterized or inferred from all publicly available nucleotide sequences. The Plant Proteome Annotation Program (PPAP) of UniProtKB/Swiss-Prot focuses on the manual annotation of plant-specific proteins and protein families. Our major effort is currently directed towards the two model plants Arabidopsis thaliana and Oryza sativa. In UniProtKB/Swiss-Prot, redundancy is minimized by merging all data from different sources in a single entry. The proposed protein sequence is frequently modified after comparison with ESTs, full length transcripts or homologous proteins from other species. The information present in manually curated entries allows the reconstruction of all described isoforms. The annotation also includes proteomics data such as PTM and protein identification MS experimental results. UniProtKB and the other products of the UniProt consortium are accessible online at www.uniprot.org. PMID:19084081

  9. The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program.

    PubMed

    Schneider, Michel; Lane, Lydie; Boutet, Emmanuel; Lieberherr, Damien; Tognolli, Michael; Bougueleret, Lydie; Bairoch, Amos

    2009-04-13

    The UniProt knowledgebase, UniProtKB, is the main product of the UniProt consortium. It consists of two sections, UniProtKB/Swiss-Prot, the manually curated section, and UniProtKB/TrEMBL, the computer translation of the EMBL/GenBank/DDBJ nucleotide sequence database. Taken together, these two sections cover all the proteins characterized or inferred from all publicly available nucleotide sequences. The Plant Proteome Annotation Program (PPAP) of UniProtKB/Swiss-Prot focuses on the manual annotation of plant-specific proteins and protein families. Our major effort is currently directed towards the two model plants Arabidopsis thaliana and Oryza sativa. In UniProtKB/Swiss-Prot, redundancy is minimized by merging all data from different sources in a single entry. The proposed protein sequence is frequently modified after comparison with ESTs, full length transcripts or homologous proteins from other species. The information present in manually curated entries allows the reconstruction of all described isoforms. The annotation also includes proteomics data such as PTM and protein identification MS experimental results. UniProtKB and the other products of the UniProt consortium are accessible online at www.uniprot.org. PMID:19084081

  10. UniProt: the Universal Protein knowledgebase

    PubMed Central

    Apweiler, Rolf; Bairoch, Amos; Wu, Cathy H.; Barker, Winona C.; Boeckmann, Brigitte; Ferro, Serenella; Gasteiger, Elisabeth; Huang, Hongzhan; Lopez, Rodrigo; Magrane, Michele; Martin, Maria J.; Natale, Darren A.; O’Donovan, Claire; Redaschi, Nicole; Yeh, Lai-Su L.

    2004-01-01

    To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, the Swiss-Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt) consortium. Our mission is to provide a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and query interfaces. The central database will have two sections, corresponding to the familiar Swiss-Prot (fully manually curated entries) and TrEMBL (enriched with automated classification, annotation and extensive cross-references). For convenient sequence searches, UniProt also provides several non-redundant sequence databases. The UniProt NREF (UniRef) databases provide representative subsets of the knowledgebase suitable for efficient searching. The comprehensive UniProt Archive (UniParc) is updated daily from many public source databases. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). The scientific community is encouraged to submit data for inclusion in UniProt. PMID:14681372

  11. UniProt: the Universal Protein knowledgebase.

    PubMed

    Apweiler, Rolf; Bairoch, Amos; Wu, Cathy H; Barker, Winona C; Boeckmann, Brigitte; Ferro, Serenella; Gasteiger, Elisabeth; Huang, Hongzhan; Lopez, Rodrigo; Magrane, Michele; Martin, Maria J; Natale, Darren A; O'Donovan, Claire; Redaschi, Nicole; Yeh, Lai-Su L

    2004-01-01

    To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, the Swiss-Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt) consortium. Our mission is to provide a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and query interfaces. The central database will have two sections, corresponding to the familiar Swiss-Prot (fully manually curated entries) and TrEMBL (enriched with automated classification, annotation and extensive cross-references). For convenient sequence searches, UniProt also provides several non-redundant sequence databases. The UniProt NREF (UniRef) databases provide representative subsets of the knowledgebase suitable for efficient searching. The comprehensive UniProt Archive (UniParc) is updated daily from many public source databases. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). The scientific community is encouraged to submit data for inclusion in UniProt. PMID:14681372

  12. The UniProtKB/Swiss-Prot Tox-Prot program: a central hub of integrated venom protein data

    PubMed Central

    Jungo, Florence; Bougueleret, Lydie; Xenarios, Ioannis; Poux, Sylvain

    2012-01-01

    Animal toxins are of interest to a wide range of scientists, due to their numerous applications in pharmacology, neurology, hematology, medicine, and drug research. This, and to a lesser extent the development of new performing tools in transcriptomics and proteomics, has led to an increase in toxin discovery. In this context, providing publicly available data on animal toxins has become essential. The UniProtKB/Swiss-Prot Tox-Prot program (http://www.uniprot.org/program/Toxins) plays a crucial role by providing such an access to venom protein sequences and functions from all venomous species. This program has up to now curated more than 5’000 venom proteins to the high-quality standards of UniProtKB/Swiss-Prot (release 2012_02). Proteins targeted by these toxins are also available in the knowledgebase. This paper describes in details the type of information provided by UniProtKB/Swiss-Prot for toxins, as well as the structured format of the knowledgebase. PMID:22465017

  13. Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase.

    PubMed

    Yip, Yum L; Famiglietti, Maria; Gos, Arnaud; Duek, Paula D; David, Fabrice P A; Gateau, Alain; Bairoch, Amos

    2008-03-01

    UniProtKB/Swiss-Prot (http://beta.uniprot.org/uniprot; last accessed: 19 October 2007) is a manually curated knowledgebase providing information on protein sequences and functional annotation. It is part of the Universal Protein Resource (UniProt). The knowledgebase currently records a total of 32,282 single amino acid polymorphisms (SAPs) touching 6,086 human proteins (Release 53.2, 26 June 2007). Nearly all SAPs are derived from literature reports using strict inclusion criteria. For each SAP, the knowledgebase provides, apart from the position of the mutation and the resulting change in amino acid, information on the effects of SAPs on protein structure and function, as well as their potential involvement in diseases. Presently, there are 16,043 disease-related SAPs, 14,266 polymorphisms, and 1,973 unclassified variants recorded in UniProtKB/Swiss-Prot. Relevant information on SAPs can be found in various sections of a UniProtKB/Swiss-Prot entry. In addition to these, cross-references to human disease databases as well as other gene-specific databases, are being added regularly. In 2003, the Swiss-Prot variant pages were created to provide a concise view of the information related to the SAPs recorded in the knowledgebase. When compared to the information on missense variants listed in other mutation databases, UniProtKB/Swiss-Prot further records information on direct protein sequencing and characterization including posttranslational modifications (PTMs). The direct links to the Online Mendelian Inheritance in Man (OMIM) database entries further enhance the integration of phenotype information with data at protein level. In this regard, SAP information in UniProtKB/Swiss-Prot complements nicely those existing in genomic and phenotypic databases, and is valuable for the understanding of SAPs and diseases. PMID:18175334

  14. The Universal Protein Resource (UniProt) in 2010

    PubMed Central

    2010-01-01

    The primary mission of UniProt is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. UniProt is produced by the UniProt Consortium which consists of groups from the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. UniProt is updated and distributed every 3 weeks and can be accessed online for searches or download at http://www.uniprot.org. PMID:19843607

  15. The Universal Protein Resource (UniProt) in 2010.

    PubMed

    2010-01-01

    The primary mission of UniProt is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. UniProt is produced by the UniProt Consortium which consists of groups from the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. UniProt is updated and distributed every 3 weeks and can be accessed online for searches or download at http://www.uniprot.org. PMID:19843607

  16. The Universal Protein Resource (UniProt) 2009.

    PubMed

    2009-01-01

    The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information that is essential for modern biological research. UniProt is produced by the UniProt Consortium which consists of groups from the European Bioinformatics Institute, the Protein Information Resource and the Swiss Institute of Bioinformatics. The core activities include manual curation of protein sequences assisted by computational analysis, sequence archiving, a user-friendly UniProt website and the provision of additional value-added information through cross-references to other databases. UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. One of the key achievements of the UniProt consortium in 2008 is the completion of the first draft of the complete human proteome in UniProtKB/Swiss-Prot. This manually annotated representation of all currently known human protein-coding genes was made available in UniProt release 14.0 with 20 325 entries. UniProt is updated and distributed every three weeks and can be accessed online for searches or downloaded at www.uniprot.org. PMID:18836194

  17. The Universal Protein Resource (UniProt) 2009

    PubMed Central

    2009-01-01

    The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information that is essential for modern biological research. UniProt is produced by the UniProt Consortium which consists of groups from the European Bioinformatics Institute, the Protein Information Resource and the Swiss Institute of Bioinformatics. The core activities include manual curation of protein sequences assisted by computational analysis, sequence archiving, a user-friendly UniProt website and the provision of additional value-added information through cross-references to other databases. UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. One of the key achievements of the UniProt consortium in 2008 is the completion of the first draft of the complete human proteome in UniProtKB/Swiss-Prot. This manually annotated representation of all currently known human protein-coding genes was made available in UniProt release 14.0 with 20 325 entries. UniProt is updated and distributed every three weeks and can be accessed online for searches or downloaded at www.uniprot.org. PMID:18836194

  18. Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase.

    PubMed

    Gaudet, P; Lane, L; Fey, P; Bridge, A; Poux, S; Auchincloss, A; Axelsen, K; Braconi Quintaje, S; Boutet, E; Brown, P; Coudert, E; Datta, R S; de Lima, W C; de Oliveira Lima, T; Duvaud, S; Farriol-Mathis, N; Ferro Rojas, S; Feuermann, M; Gateau, A; Hinz, U; Hulo, C; James, J; Jimenez, S; Jungo, F; Keller, G; Lemercier, P; Lieberherr, D; Moinat, M; Nikolskaya, A; Pedruzzi, I; Rivoire, C; Roechert, B; Schneider, M; Stanley, E; Tognolli, M; Sjölander, K; Bougueleret, L; Chisholm, R L; Bairoch, A

    2009-01-01

    UniProtKB/Swiss-Prot, a curated protein database, and dictyBase, the Model Organism Database for Dictyostelium discoideum, have established a collaboration to improve data sharing. One of the major steps in this effort was the 'Dicty annotation marathon', a week-long exercise with 30 annotators aimed at achieving a major increase in the number of D. discoideum proteins represented in UniProtKB/Swiss-Prot. The marathon led to the annotation of over 1000 D. discoideum proteins in UniProtKB/Swiss-Prot. Concomitantly, there were a large number of updates in dictyBase concerning gene symbols, protein names and gene models. This exercise demonstrates how UniProtKB/Swiss-Prot can work in very close cooperation with model organism databases and how the annotation of proteins can be accelerated through those collaborations. PMID:20157489

  19. Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase

    PubMed Central

    Gaudet, P.; Lane, L.; Fey, P.; Bridge, A.; Poux, S.; Auchincloss, A.; Axelsen, K.; Braconi Quintaje, S.; Boutet, E.; Brown, P.; Coudert, E.; Datta, R.S.; de Lima, W.C.; de Oliveira Lima, T.; Duvaud, S.; Farriol-Mathis, N.; Ferro Rojas, S.; Feuermann, M.; Gateau, A.; Hinz, U.; Hulo, C.; James, J.; Jimenez, S.; Jungo, F.; Keller, G.; Lemercier, P.; Lieberherr, D.; Moinat, M.; Nikolskaya, A.; Pedruzzi, I.; Rivoire, C.; Roechert, B.; Schneider, M.; Stanley, E.; Tognolli, M.; Sjölander, K.; Bougueleret, L.; Chisholm, R.L.; Bairoch, A.

    2009-01-01

    UniProtKB/Swiss-Prot, a curated protein database, and dictyBase, the Model Organism Database for Dictyostelium discoideum, have established a collaboration to improve data sharing. One of the major steps in this effort was the ‘Dicty annotation marathon’, a week-long exercise with 30 annotators aimed at achieving a major increase in the number of D. discoideum proteins represented in UniProtKB/Swiss-Prot. The marathon led to the annotation of over 1000 D. discoideum proteins in UniProtKB/Swiss-Prot. Concomitantly, there were a large number of updates in dictyBase concerning gene symbols, protein names and gene models. This exercise demonstrates how UniProtKB/Swiss-Prot can work in very close cooperation with model organism databases and how the annotation of proteins can be accelerated through those collaborations. PMID:20157489

  20. Plant Protein Annotation in the UniProt Knowledgebase1

    PubMed Central

    Schneider, Michel; Bairoch, Amos; Wu, Cathy H.; Apweiler, Rolf

    2005-01-01

    The Swiss-Prot, TrEMBL, Protein Information Resource (PIR), and DNA Data Bank of Japan (DDBJ) protein database activities have united to form the Universal Protein Resource (UniProt) Consortium. UniProt presents three database layers: the UniProt Archive, the UniProt Knowledgebase (UniProtKB), and the UniProt Reference Clusters. The UniProtKB consists of two sections: UniProtKB/Swiss-Prot (fully manually curated entries) and UniProtKB/TrEMBL (automated annotation, classification and extensive cross-references). New releases are published fortnightly. A specific Plant Proteome Annotation Program (http://www.expasy.org/sprot/ppap/) was initiated to cope with the increasing amount of data produced by the complete sequencing of plant genomes. Through UniProt, our aim is to provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information that will allow the plant community to fully explore and utilize the wealth of information available for both plant and nonplant model organisms. PMID:15888679

  1. Plant protein annotation in the UniProt Knowledgebase.

    PubMed

    Schneider, Michel; Bairoch, Amos; Wu, Cathy H; Apweiler, Rolf

    2005-05-01

    The Swiss-Prot, TrEMBL, Protein Information Resource (PIR), and DNA Data Bank of Japan (DDBJ) protein database activities have united to form the Universal Protein Resource (UniProt) Consortium. UniProt presents three database layers: the UniProt Archive, the UniProt Knowledgebase (UniProtKB), and the UniProt Reference Clusters. The UniProtKB consists of two sections: UniProtKB/Swiss-Prot (fully manually curated entries) and UniProtKB/TrEMBL (automated annotation, classification and extensive cross-references). New releases are published fortnightly. A specific Plant Proteome Annotation Program (http://www.expasy.org/sprot/ppap/) was initiated to cope with the increasing amount of data produced by the complete sequencing of plant genomes. Through UniProt, our aim is to provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information that will allow the plant community to fully explore and utilize the wealth of information available for both plant and non-plant model organisms. PMID:15888679

  2. Tox-Prot, the toxin protein annotation program of the Swiss-Prot protein knowledgebase.

    PubMed

    Jungo, Florence; Bairoch, Amos

    2005-03-01

    The Tox-Prot program was initiated in order to provide the scientific community a summary of the current knowledge on animal protein toxins. The aim of this program is to systematically annotate all proteins which act as toxins and are produced by venomous and poisonous animals. Venomous animals such as snakes, scorpions, spiders, jellyfish, insects, cone snails, sea anemones, lizards, some fish, and platypus are equipped with a specialized organ to inject venom in their prey. In contrast, poisonous animals such as some fish or worms, lack such organs. Each toxin is annotated according to the quality standards of Swiss-Prot. This means providing a wealth of information that includes the description of the function, domain structure, subcellular location, tissue specificity, variants, similarities to other proteins, keywords, etc. In the framework of this program, particular care has been made to capture what is known on the function and mode of action, posttranslational modifications and 3D structural data which are all relatively abundant in the field of protein toxins. Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to Swiss-Prot concerning toxins at Tox-Prot@isb-sib.ch. More information on Tox-Prot can be found at http://www.expasy.org/sprot/tox-prot. PMID:15683867

  3. neXtProt: a knowledge platform for human proteins.

    PubMed

    Lane, Lydie; Argoud-Puy, Ghislaine; Britan, Aurore; Cusin, Isabelle; Duek, Paula D; Evalet, Olivier; Gateau, Alain; Gaudet, Pascale; Gleizes, Anne; Masselot, Alexandre; Zwahlen, Catherine; Bairoch, Amos

    2012-01-01

    neXtProt (http://www.nextprot.org/) is a new human protein-centric knowledge platform. Developed at the Swiss Institute of Bioinformatics (SIB), it aims to help researchers answer questions relevant to human proteins. To achieve this goal, neXtProt is built on a corpus containing both curated knowledge originating from the UniProtKB/Swiss-Prot knowledgebase and carefully selected and filtered high-throughput data pertinent to human proteins. This article presents an overview of the database and the data integration process. We also lay out the key future directions of neXtProt that we consider the necessary steps to make neXtProt the one-stop-shop for all research projects focusing on human proteins. PMID:22139911

  4. neXtProt: a knowledge platform for human proteins

    PubMed Central

    Lane, Lydie; Argoud-Puy, Ghislaine; Britan, Aurore; Cusin, Isabelle; Duek, Paula D.; Evalet, Olivier; Gateau, Alain; Gaudet, Pascale; Gleizes, Anne; Masselot, Alexandre; Zwahlen, Catherine; Bairoch, Amos

    2012-01-01

    neXtProt (http://www.nextprot.org/) is a new human protein-centric knowledge platform. Developed at the Swiss Institute of Bioinformatics (SIB), it aims to help researchers answer questions relevant to human proteins. To achieve this goal, neXtProt is built on a corpus containing both curated knowledge originating from the UniProtKB/Swiss-Prot knowledgebase and carefully selected and filtered high-throughput data pertinent to human proteins. This article presents an overview of the database and the data integration process. We also lay out the key future directions of neXtProt that we consider the necessary steps to make neXtProt the one-stop-shop for all research projects focusing on human proteins. PMID:22139911

  5. The SWISS-PROT protein sequence data bank: current status.

    PubMed Central

    Bairoch, A; Boeckmann, B

    1994-01-01

    SWISS-PROT is an annotated protein sequence database established in 1986 and maintained collaboratively, since 1988, by the Department of Medical Biochemistry of the University of Geneva and the EMBL Data Library. The SWISS-PROT protein sequence data bank consist of sequence entries. Sequence entries are composed of different lines types, each with their own format. For standardization purposes the format of SWISS-PROT follows as closely as possible that of the EMBL Nucleotide Sequence Database. A sample SWISS-PROT entry is shown in Figure 1. PMID:7937062

  6. ENZYMAP: Exploiting Protein Annotation for Modeling and Predicting EC Number Changes in UniProt/Swiss-Prot

    PubMed Central

    Silveira, Sabrina de Azevedo; de Melo-Minardi, Raquel Cardoso; da Silveira, Carlos Henrique; Santoro, Marcelo Matos; Meira Jr, Wagner

    2014-01-01

    The volume and diversity of biological data are increasing at very high rates. Vast amounts of protein sequences and structures, protein and genetic interactions and phenotype studies have been produced. The majority of data generated by high-throughput devices is automatically annotated because manually annotating them is not possible. Thus, efficient and precise automatic annotation methods are required to ensure the quality and reliability of both the biological data and associated annotations. We proposed ENZYMatic Annotation Predictor (ENZYMAP), a technique to characterize and predict EC number changes based on annotations from UniProt/Swiss-Prot using a supervised learning approach. We evaluated ENZYMAP experimentally, using test data sets from both UniProt/Swiss-Prot and UniProt/TrEMBL, and showed that predicting EC changes using selected types of annotation is possible. Finally, we compared ENZYMAP and DETECT with respect to their predictions and checked both against the UniProt/Swiss-Prot annotations. ENZYMAP was shown to be more accurate than DETECT, coming closer to the actual changes in UniProt/Swiss-Prot. Our proposal is intended to be an automatic complementary method (that can be used together with other techniques like the ones based on protein sequence and structure) that helps to improve the quality and reliability of enzyme annotations over time, suggesting possible corrections, anticipating annotation changes and propagating the implicit knowledge for the whole dataset. PMID:24586563

  7. The Annotation of Both Human and Mouse Kinomes in UniProtKB/Swiss-Prot

    PubMed Central

    Quintaje, Silvia Braconi; Orchard, Sandra

    2008-01-01

    Biomolecule phosphorylation by protein kinases is a fundamental cell signaling process in all living cells. Following the comprehensive cataloguing of the protein kinase complement of the human genome (Manning, G., Whyte, D. B., Martinez, R., Hunter, T., and Sudarsanam, S. (2002) The protein kinase complement of the human genome. Science 298, 1912–1934), this review will detail the state-of-the-art human and mouse kinase proteomes as provided in the UniProtKB/Swiss-Prot protein knowledgebase. The sequences of the 480 classical and up to 24 atypical protein kinases now believed to exist in the human genome and 484 classical and up to 24 atypical kinases within the mouse genome have been reviewed and, where necessary, revised. Extensive annotation has been added to each entry. In an era when a wealth of new databases is emerging on the Internet, UniProtKB/Swiss-Prot makes available to the scientific community the most up-to-date and in-depth annotation of these proteins with access to additional external resources linked from within each entry. Incorrect sequence annotations resulting from errors and artifacts have been eliminated. Each entry will be constantly reviewed and updated as new information becomes available with the orthologous enzymes in related species being annotated in a parallel effort and complete kinomes being completed as sequences become available. This ensures that the mammalian kinomes available from UniProtKB/Swiss-Prot are of a consistently high standard with each separate entry acting both as a valuable information resource and a central portal to a wealth of further detail via extensive cross-referencing. PMID:18436524

  8. Activities at the Universal Protein Resource (UniProt)

    PubMed Central

    2014-01-01

    The mission of the Universal Protein Resource (UniProt) (http://www.uniprot.org) is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequences and functional annotation. It integrates, interprets and standardizes data from literature and numerous resources to achieve the most comprehensive catalog possible of protein information. The central activities are the biocuration of the UniProt Knowledgebase and the dissemination of these data through our Web site and web services. UniProt is produced by the UniProt Consortium, which consists of groups from the European Bioinformatics Institute (EBI), the SIB Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is updated and distributed every 4 weeks and can be accessed online for searches or downloads. PMID:24253303

  9. UniProt Knowledgebase: a hub of integrated protein data

    PubMed Central

    Magrane, Michele; Consortium, UniProt

    2011-01-01

    The UniProt Knowledgebase (UniProtKB) acts as a central hub of protein knowledge by providing a unified view of protein sequence and functional information. Manual and automatic annotation procedures are used to add data directly to the database while extensive cross-referencing to more than 120 external databases provides access to additional relevant information in more specialized data collections. UniProtKB also integrates a range of data from other resources. All information is attributed to its original source, allowing users to trace the provenance of all data. The UniProt Consortium is committed to using and promoting common data exchange formats and technologies, and UniProtKB data is made freely available in a range of formats to facilitate integration with other databases. Database URL: http://www.uniprot.org/ PMID:21447597

  10. UniProt Knowledgebase: a hub of integrated protein data.

    PubMed

    Magrane, Michele

    2011-01-01

    The UniProt Knowledgebase (UniProtKB) acts as a central hub of protein knowledge by providing a unified view of protein sequence and functional information. Manual and automatic annotation procedures are used to add data directly to the database while extensive cross-referencing to more than 120 external databases provides access to additional relevant information in more specialized data collections. UniProtKB also integrates a range of data from other resources. All information is attributed to its original source, allowing users to trace the provenance of all data. The UniProt Consortium is committed to using and promoting common data exchange formats and technologies, and UniProtKB data is made freely available in a range of formats to facilitate integration with other databases. Database URL: http://www.uniprot.org/ PMID:21447597

  11. The UniProtKB guide to the human proteome

    PubMed Central

    Breuza, Lionel; Poux, Sylvain; Estreicher, Anne; Famiglietti, Maria Livia; Magrane, Michele; Tognolli, Michael; Bridge, Alan; Baratin, Delphine; Redaschi, Nicole

    2016-01-01

    Advances in high-throughput and advanced technologies allow researchers to routinely perform whole genome and proteome analysis. For this purpose, they need high-quality resources providing comprehensive gene and protein sets for their organisms of interest. Using the example of the human proteome, we will describe the content of a complete proteome in the UniProt Knowledgebase (UniProtKB). We will show how manual expert curation of UniProtKB/Swiss-Prot is complemented by expert-driven automatic annotation to build a comprehensive, high-quality and traceable resource. We will also illustrate how the complexity of the human proteome is captured and structured in UniProtKB. Database URL: www.uniprot.org PMID:26896845

  12. Update on activities at the Universal Protein Resource (UniProt) in 2013

    PubMed Central

    2013-01-01

    The mission of the Universal Protein Resource (UniProt) (http://www.uniprot.org) is to support biological research by providing a freely accessible, stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase. It integrates, interprets and standardizes data from numerous resources to achieve the most comprehensive catalogue of protein sequences and functional annotation. UniProt comprises four major components, each optimized for different uses, the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. UniProt is produced by the UniProt Consortium, which consists of groups from the European Bioinformatics Institute (EBI), the SIB Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is updated and distributed every 4 weeks and can be accessed online for searches or downloads. PMID:23161681

  13. The UniProt-GO Annotation database in 2011

    PubMed Central

    Dimmer, Emily C.; Huntley, Rachael P.; Alam-Faruque, Yasmin; Sawford, Tony; O'Donovan, Claire; Martin, Maria J.; Bely, Benoit; Browne, Paul; Mun Chan, Wei; Eberhardt, Ruth; Gardner, Michael; Laiho, Kati; Legge, Duncan; Magrane, Michele; Pichler, Klemens; Poggioli, Diego; Sehra, Harminder; Auchincloss, Andrea; Axelsen, Kristian; Blatter, Marie-Claude; Boutet, Emmanuel; Braconi-Quintaje, Silvia; Breuza, Lionel; Bridge, Alan; Coudert, Elizabeth; Estreicher, Anne; Famiglietti, Livia; Ferro-Rojas, Serenella; Feuermann, Marc; Gos, Arnaud; Gruaz-Gumowski, Nadine; Hinz, Ursula; Hulo, Chantal; James, Janet; Jimenez, Silvia; Jungo, Florence; Keller, Guillaume; Lemercier, Phillippe; Lieberherr, Damien; Masson, Patrick; Moinat, Madelaine; Pedruzzi, Ivo; Poux, Sylvain; Rivoire, Catherine; Roechert, Bernd; Schneider, Michael; Stutz, Andre; Sundaram, Shyamala; Tognolli, Michael; Bougueleret, Lydie; Argoud-Puy, Ghislaine; Cusin, Isabelle; Duek- Roggli, Paula; Xenarios, Ioannis; Apweiler, Rolf

    2012-01-01

    The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360 000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set. PMID:22123736

  14. The UniProt-GO Annotation database in 2011.

    PubMed

    Dimmer, Emily C; Huntley, Rachael P; Alam-Faruque, Yasmin; Sawford, Tony; O'Donovan, Claire; Martin, Maria J; Bely, Benoit; Browne, Paul; Mun Chan, Wei; Eberhardt, Ruth; Gardner, Michael; Laiho, Kati; Legge, Duncan; Magrane, Michele; Pichler, Klemens; Poggioli, Diego; Sehra, Harminder; Auchincloss, Andrea; Axelsen, Kristian; Blatter, Marie-Claude; Boutet, Emmanuel; Braconi-Quintaje, Silvia; Breuza, Lionel; Bridge, Alan; Coudert, Elizabeth; Estreicher, Anne; Famiglietti, Livia; Ferro-Rojas, Serenella; Feuermann, Marc; Gos, Arnaud; Gruaz-Gumowski, Nadine; Hinz, Ursula; Hulo, Chantal; James, Janet; Jimenez, Silvia; Jungo, Florence; Keller, Guillaume; Lemercier, Phillippe; Lieberherr, Damien; Masson, Patrick; Moinat, Madelaine; Pedruzzi, Ivo; Poux, Sylvain; Rivoire, Catherine; Roechert, Bernd; Schneider, Michael; Stutz, Andre; Sundaram, Shyamala; Tognolli, Michael; Bougueleret, Lydie; Argoud-Puy, Ghislaine; Cusin, Isabelle; Duek-Roggli, Paula; Xenarios, Ioannis; Apweiler, Rolf

    2012-01-01

    The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360,000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set. PMID:22123736

  15. Reorganizing the protein space at the Universal Protein Resource (UniProt)

    PubMed Central

    2012-01-01

    The mission of UniProt is to support biological research by providing a freely accessible, stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces. UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. A key development at UniProt is the provision of complete, reference and representative proteomes. UniProt is updated and distributed every 4 weeks and can be accessed online for searches or download at http://www.uniprot.org. PMID:22102590

  16. Reorganizing the protein space at the Universal Protein Resource (UniProt).

    PubMed

    2012-01-01

    The mission of UniProt is to support biological research by providing a freely accessible, stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces. UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. A key development at UniProt is the provision of complete, reference and representative proteomes. UniProt is updated and distributed every 4 weeks and can be accessed online for searches or download at http://www.uniprot.org. PMID:22102590

  17. 48 CFR 719.273-5 - Selection of Protégé firms.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... (USAID) Mentor-Protégé Program 719.273-5 Selection of Protégé firms. (a) Mentor firms will be solely responsible for selecting Protégé firms. Mentors are encouraged to select from a broad base of small business.... (b) Mentors may have multiple Protégés. However, to preserve the integrity of the Program and...

  18. 48 CFR 819.7111 - Obligations under the Mentor-Protégé Program.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... Mentor-Protégé Program. 819.7111 Section 819.7111 Federal Acquisition Regulations System DEPARTMENT OF VETERANS AFFAIRS SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS VA Mentor-Protégé Program 819.7111 Obligations under the Mentor-Protégé Program. (a) A mentor or protégé may voluntarily withdraw from...

  19. 48 CFR 719.273-5 - Selection of Protégé firms.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... (USAID) Mentor-Protégé Program 719.273-5 Selection of Protégé firms. (a) Mentor firms will be solely responsible for selecting Protégé firms. Mentors are encouraged to select from a broad base of small business.... (b) Mentors may have multiple Protégés. However, to preserve the integrity of the Program and...

  20. 48 CFR 719.273-9 - Obligations under the Mentor-Protégé Program.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... Mentor-Protégé Program. 719.273-9 Section 719.273-9 Federal Acquisition Regulations System AGENCY FOR... Development (USAID) Mentor-Protégé Program 719.273-9 Obligations under the Mentor-Protégé Program. (a) A Mentor or Protégé may voluntarily withdraw from the Program. However, in no event shall such...

  1. 48 CFR 819.7111 - Obligations under the Mentor-Protégé Program.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Mentor-Protégé Program. 819.7111 Section 819.7111 Federal Acquisition Regulations System DEPARTMENT OF VETERANS AFFAIRS SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS VA Mentor-Protégé Program 819.7111 Obligations under the Mentor-Protégé Program. (a) A mentor or protégé may voluntarily withdraw from...

  2. 48 CFR 719.273-5 - Selection of Protégé firms.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... (USAID) Mentor-Protégé Program 719.273-5 Selection of Protégé firms. (a) Mentor firms will be solely responsible for selecting Protégé firms. Mentors are encouraged to select from a broad base of small business.... (b) Mentors may have multiple Protégés. However, to preserve the integrity of the Program and...

  3. 48 CFR 819.7111 - Obligations under the Mentor-Protégé Program.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... Mentor-Protégé Program. 819.7111 Section 819.7111 Federal Acquisition Regulations System DEPARTMENT OF VETERANS AFFAIRS SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS VA Mentor-Protégé Program 819.7111 Obligations under the Mentor-Protégé Program. (a) A mentor or protégé may voluntarily withdraw from...

  4. 48 CFR 719.273-9 - Obligations under the Mentor-Protégé Program.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Mentor-Protégé Program. 719.273-9 Section 719.273-9 Federal Acquisition Regulations System AGENCY FOR... Development (USAID) Mentor-Protégé Program 719.273-9 Obligations under the Mentor-Protégé Program. (a) A Mentor or Protégé may voluntarily withdraw from the Program. However, in no event shall such...

  5. 48 CFR 819.7107 - Selection of Protégé firms.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS VA Mentor-Protégé Program 819.7107 Selection of Protégé firms. (a) Mentor firms will be solely responsible for selecting protégé firms. Mentors are encouraged to.... (b) Mentors may have multiple protégés. However, to preserve the integrity of the Program and...

  6. 48 CFR 719.273-9 - Obligations under the Mentor-Protégé Program.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... Mentor-Protégé Program. 719.273-9 Section 719.273-9 Federal Acquisition Regulations System AGENCY FOR... Development (USAID) Mentor-Protégé Program 719.273-9 Obligations under the Mentor-Protégé Program. (a) A Mentor or Protégé may voluntarily withdraw from the Program. However, in no event shall such...

  7. 48 CFR 719.273-9 - Obligations under the Mentor-Protégé Program.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... Mentor-Protégé Program. 719.273-9 Section 719.273-9 Federal Acquisition Regulations System AGENCY FOR... Development (USAID) Mentor-Protégé Program 719.273-9 Obligations under the Mentor-Protégé Program. (a) A Mentor or Protégé may voluntarily withdraw from the Program. However, in no event shall such...

  8. 48 CFR 819.7107 - Selection of Protégé firms.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS VA Mentor-Protégé Program 819.7107 Selection of Protégé firms. (a) Mentor firms will be solely responsible for selecting protégé firms. Mentors are encouraged to.... (b) Mentors may have multiple protégés. However, to preserve the integrity of the Program and...

  9. 48 CFR 719.273-9 - Obligations under the Mentor-Protégé Program.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... Mentor-Protégé Program. 719.273-9 Section 719.273-9 Federal Acquisition Regulations System AGENCY FOR... Development (USAID) Mentor-Protégé Program 719.273-9 Obligations under the Mentor-Protégé Program. (a) A Mentor or Protégé may voluntarily withdraw from the Program. However, in no event shall such...

  10. 48 CFR 819.7111 - Obligations under the Mentor-Protégé Program.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... Mentor-Protégé Program. 819.7111 Section 819.7111 Federal Acquisition Regulations System DEPARTMENT OF VETERANS AFFAIRS SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS VA Mentor-Protégé Program 819.7111 Obligations under the Mentor-Protégé Program. (a) A mentor or protégé may voluntarily withdraw from...

  11. 48 CFR 719.273-5 - Selection of Protégé firms.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... (USAID) Mentor-Protégé Program 719.273-5 Selection of Protégé firms. (a) Mentor firms will be solely responsible for selecting Protégé firms. Mentors are encouraged to select from a broad base of small business.... (b) Mentors may have multiple Protégés. However, to preserve the integrity of the Program and...

  12. 48 CFR 819.7111 - Obligations under the Mentor-Protégé Program.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... Mentor-Protégé Program. 819.7111 Section 819.7111 Federal Acquisition Regulations System DEPARTMENT OF VETERANS AFFAIRS SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS VA Mentor-Protégé Program 819.7111 Obligations under the Mentor-Protégé Program. (a) A mentor or protégé may voluntarily withdraw from...

  13. 48 CFR 819.7107 - Selection of Protégé firms.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS VA Mentor-Protégé Program 819.7107 Selection of Protégé firms. (a) Mentor firms will be solely responsible for selecting protégé firms. Mentors are encouraged to.... (b) Mentors may have multiple protégés. However, to preserve the integrity of the Program and...

  14. 48 CFR 819.7107 - Selection of Protégé firms.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS VA Mentor-Protégé Program 819.7107 Selection of Protégé firms. (a) Mentor firms will be solely responsible for selecting protégé firms. Mentors are encouraged to.... (b) Mentors may have multiple protégés. However, to preserve the integrity of the Program and...

  15. 48 CFR 819.7107 - Selection of Protégé firms.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS VA Mentor-Protégé Program 819.7107 Selection of Protégé firms. (a) Mentor firms will be solely responsible for selecting protégé firms. Mentors are encouraged to.... (b) Mentors may have multiple protégés. However, to preserve the integrity of the Program and...

  16. 48 CFR 519.7008 - Selection of protégé firms.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS GSA Mentor-Protégé Program 519.7008 Selection of protégé firms. (a) Mentor firms will be solely responsible for selecting protégé firms. Mentors are encouraged to... subcontractor or a newly selected subcontractor for the prime contractor's GSA contract. (b) Mentor firms...

  17. 48 CFR 352.219-70 - Mentor-protégé program.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 4 2014-10-01 2014-10-01 false Mentor-protégé program... Mentor-protégé program. As prescribed in 319.270-1(a), the Contracting Officer shall insert the following provision: Mentor-Protégé Program (January 2010) (a) Large business prime contractors serving as mentors...

  18. 48 CFR 519.7008 - Selection of protégé firms.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS GSA Mentor-Protégé Program 519.7008 Selection of protégé firms. (a) Mentor firms will be solely responsible for selecting protégé firms. Mentors are encouraged to... subcontractor or a newly selected subcontractor for the prime contractor's GSA contract. (b) Mentor firms...

  19. 48 CFR 352.219-70 - Mentor-protégé program.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 4 2011-10-01 2011-10-01 false Mentor-protégé program... Mentor-protégé program. As prescribed in 319.270-1(a), the Contracting Officer shall insert the following provision: Mentor-Protégé Program (January 2010) (a) Large business prime contractors serving as mentors...

  20. 48 CFR 352.219-70 - Mentor-protégé program.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 4 2010-10-01 2010-10-01 false Mentor-protégé program... Mentor-protégé program. As prescribed in 319.270-1(a), the Contracting Officer shall insert the following provision: Mentor-Protégé Program (January 2010) (a) Large business prime contractors serving as mentors...

  1. 48 CFR 352.219-71 - Mentor-protégé program reporting requirements.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 4 2014-10-01 2014-10-01 false Mentor-protégé program... Clauses 352.219-71 Mentor-protégé program reporting requirements. As prescribed in 319.270-1(b), the Contracting Officer shall insert the following clause: Mentor-Protégé Program Reporting Requirements...

  2. 48 CFR 552.219-75 - GSA Mentor-Protégé Program.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 4 2012-10-01 2012-10-01 false GSA Mentor-ProtégÃ....219-75 GSA Mentor-Protégé Program. As prescribed in 519.7017(a), insert the following clause: GSA Mentor-ProtéGé Program (SEP 2009) (a) Prime contractors, including small businesses, are encouraged...

  3. 48 CFR 1819.7205 - Mentor-protégé agreements.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 6 2014-10-01 2014-10-01 false Mentor-protégÃ... ADMINISTRATION SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS NASA Mentor-Protégé Program 1819.7205 Mentor-protégé agreements. (a) The agreements shall be structured after the mentor completes an assessment of...

  4. 48 CFR 352.219-71 - Mentor-protégé program reporting requirements.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 4 2011-10-01 2011-10-01 false Mentor-protégé program... Clauses 352.219-71 Mentor-protégé program reporting requirements. As prescribed in 319.270-1(b), the Contracting Officer shall insert the following clause: Mentor-Protégé Program Reporting Requirements...

  5. 48 CFR 352.219-70 - Mentor-protégé program.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 4 2013-10-01 2013-10-01 false Mentor-protégé program... Mentor-protégé program. As prescribed in 319.270-1(a), the Contracting Officer shall insert the following provision: Mentor-Protégé Program (January 2010) (a) Large business prime contractors serving as mentors...

  6. 48 CFR 1819.7205 - Mentor-protégé agreements.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 6 2013-10-01 2013-10-01 false Mentor-protégÃ... ADMINISTRATION SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS NASA Mentor-Protégé Program 1819.7205 Mentor-protégé agreements. (a) The agreements shall be structured after the mentor completes an assessment of...

  7. 48 CFR 519.7008 - Selection of protégé firms.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS GSA Mentor-Protégé Program 519.7008 Selection of protégé firms. (a) Mentor firms will be solely responsible for selecting protégé firms. Mentors are encouraged to... subcontractor or a newly selected subcontractor for the prime contractor's GSA contract. (b) Mentor firms...

  8. 48 CFR 552.219-75 - GSA Mentor-Protégé Program.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 4 2011-10-01 2011-10-01 false GSA Mentor-ProtégÃ....219-75 GSA Mentor-Protégé Program. As prescribed in 519.7017(a), insert the following clause: GSA Mentor-ProtéGé Program (SEP 2009) (a) Prime contractors, including small businesses, are encouraged...

  9. 48 CFR 352.219-71 - Mentor-protégé program reporting requirements.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 4 2012-10-01 2012-10-01 false Mentor-protégé program... Clauses 352.219-71 Mentor-protégé program reporting requirements. As prescribed in 319.270-1(b), the Contracting Officer shall insert the following clause: Mentor-Protégé Program Reporting Requirements...

  10. 48 CFR 552.219-75 - GSA Mentor-Protégé Program.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 4 2010-10-01 2010-10-01 false GSA Mentor-ProtégÃ....219-75 GSA Mentor-Protégé Program. As prescribed in 519.7017(a), insert the following clause: GSA Mentor-ProtéGé Program (SEP 2009) (a) Prime contractors, including small businesses, are encouraged...

  11. 48 CFR 1819.7205 - Mentor-protégé agreements.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 6 2012-10-01 2012-10-01 false Mentor-protégÃ... ADMINISTRATION SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS NASA Mentor-Protégé Program 1819.7205 Mentor-protégé agreements. (a) The agreements shall be structured after the mentor completes an assessment of...

  12. 48 CFR 519.7008 - Selection of protégé firms.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS GSA Mentor-Protégé Program 519.7008 Selection of protégé firms. (a) Mentor firms will be solely responsible for selecting protégé firms. Mentors are encouraged to... subcontractor or a newly selected subcontractor for the prime contractor's GSA contract. (b) Mentor firms...

  13. 48 CFR 352.219-70 - Mentor-protégé program.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 4 2012-10-01 2012-10-01 false Mentor-protégé program... Mentor-protégé program. As prescribed in 319.270-1(a), the Contracting Officer shall insert the following provision: Mentor-Protégé Program (January 2010) (a) Large business prime contractors serving as mentors...

  14. 48 CFR 352.219-71 - Mentor-protégé program reporting requirements.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 4 2013-10-01 2013-10-01 false Mentor-protégé program... Clauses 352.219-71 Mentor-protégé program reporting requirements. As prescribed in 319.270-1(b), the Contracting Officer shall insert the following clause: Mentor-Protégé Program Reporting Requirements...

  15. 48 CFR 552.219-75 - GSA Mentor-Protégé Program.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 4 2013-10-01 2013-10-01 false GSA Mentor-ProtégÃ....219-75 GSA Mentor-Protégé Program. As prescribed in 519.7017(a), insert the following clause: GSA Mentor-ProtéGé Program (SEP 2009) (a) Prime contractors, including small businesses, are encouraged...

  16. 48 CFR 1819.7205 - Mentor-protégé agreements.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 6 2011-10-01 2011-10-01 false Mentor-protégÃ... ADMINISTRATION SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS NASA Mentor-Protégé Program 1819.7205 Mentor-protégé agreements. (a) The agreements shall be structured after the mentor completes an assessment of...

  17. 48 CFR 552.219-75 - GSA Mentor-Protégé Program.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 4 2014-10-01 2014-10-01 false GSA Mentor-ProtégÃ....219-75 GSA Mentor-Protégé Program. As prescribed in 519.7017(a), insert the following clause: GSA Mentor-ProtéGé Program (SEP 2009) (a) Prime contractors, including small businesses, are encouraged...

  18. 48 CFR 519.7008 - Selection of protégé firms.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS GSA Mentor-Protégé Program 519.7008 Selection of protégé firms. (a) Mentor firms will be solely responsible for selecting protégé firms. Mentors are encouraged to... subcontractor or a newly selected subcontractor for the prime contractor's GSA contract. (b) Mentor firms...

  19. 48 CFR 352.219-71 - Mentor-protégé program reporting requirements.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 4 2010-10-01 2010-10-01 false Mentor-protégé program... Clauses 352.219-71 Mentor-protégé program reporting requirements. As prescribed in 319.270-1(b), the Contracting Officer shall insert the following clause: Mentor-Protégé Program Reporting Requirements...

  20. Genetic Variations and Diseases in UniProtKB/Swiss-Prot: The Ins and Outs of Expert Manual Curation

    PubMed Central

    Famiglietti, Maria Livia; Estreicher, Anne; Gos, Arnaud; Bolleman, Jerven; Géhant, Sébastien; Breuza, Lionel; Bridge, Alan; Poux, Sylvain; Redaschi, Nicole; Bougueleret, Lydie; Xenarios, Ioannis

    2014-01-01

    During the last few years, next-generation sequencing (NGS) technologies have accelerated the detection of genetic variants resulting in the rapid discovery of new disease-associated genes. However, the wealth of variation data made available by NGS alone is not sufficient to understand the mechanisms underlying disease pathogenesis and manifestation. Multidisciplinary approaches combining sequence and clinical data with prior biological knowledge are needed to unravel the role of genetic variants in human health and disease. In this context, it is crucial that these data are linked, organized, and made readily available through reliable online resources. The Swiss-Prot section of the Universal Protein Knowledgebase (UniProtKB/Swiss-Prot) provides the scientific community with a collection of information on protein functions, interactions, biological pathways, as well as human genetic diseases and variants, all manually reviewed by experts. In this article, we present an overview of the information content of UniProtKB/Swiss-Prot to show how this knowledgebase can support researchers in the elucidation of the mechanisms leading from a molecular defect to a disease phenotype. PMID:24848695

  1. Annotation of glycoproteins in the SWISS-PROT database.

    PubMed

    Jung, E; Veuthey, A L; Gasteiger, E; Bairoch, A

    2001-02-01

    SWISS-PROT is a protein sequence database, which aims to be nonredundant, fully annotated and highly cross-referenced. Most eukaryotic gene products undergo co- and/or post-translational modifications, and these need to be included in the database in order to describe the mature protein. SWISS-PROT includes information on many types of different protein modifications. As glycosylation is the most common type of post-translational protein modification, we are currently placing an emphasis on annotation of protein glycosylation in SWISS-PROT. Information on the position of the sugar within the polypeptide chain, the reducing terminal linkage as well as additional information on biological function of the sugar is included in the database. In this paper we describe how we account for the different types of protein glycosylation, namely N-linked glycosylation, O-linked glycosylation, proteoglycans, C-linked glycosylation and the attachment of glycosyl-phosphatidylinosital anchors to proteins. PMID:11680872

  2. The Universal Protein Resource (UniProt): an expanding universe of protein information.

    PubMed

    Wu, Cathy H; Apweiler, Rolf; Bairoch, Amos; Natale, Darren A; Barker, Winona C; Boeckmann, Brigitte; Ferro, Serenella; Gasteiger, Elisabeth; Huang, Hongzhan; Lopez, Rodrigo; Magrane, Michele; Martin, Maria J; Mazumder, Raja; O'Donovan, Claire; Redaschi, Nicole; Suzek, Baris

    2006-01-01

    The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics. The UniProt Knowledgebase (UniProtKB), comprising the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniProtKB/TrEMBL section, is the preeminent storehouse of protein annotation. The extensive cross-references, functional and feature annotations and literature-based evidence attribution enable scientists to analyse proteins and query across databases. The UniProt Reference Clusters (UniRef) speed similarity searches via sequence space compression by merging sequences that are 100% (UniRef100), 90% (UniRef90) or 50% (UniRef50) identical. Finally, the UniProt Archive (UniParc) stores all publicly available protein sequences, containing the history of sequence data with links to the source databases. UniProt databases continue to grow in size and in availability of information. Recent and upcoming changes to database contents, formats, controlled vocabularies and services are described. New download availability includes all major releases of UniProtKB, sequence collections by taxonomic division and complete proteomes. A bibliography mapping service has been added, and an ID mapping service will be available soon. UniProt databases can be accessed online at http://www.uniprot.org or downloaded at ftp://ftp.uniprot.org/pub/databases/. PMID:16381842

  3. The Universal Protein Resource (UniProt): an expanding universe of protein information

    PubMed Central

    Wu, Cathy H.; Apweiler, Rolf; Bairoch, Amos; Natale, Darren A.; Barker, Winona C.; Boeckmann, Brigitte; Ferro, Serenella; Gasteiger, Elisabeth; Huang, Hongzhan; Lopez, Rodrigo; Magrane, Michele; Martin, Maria J.; Mazumder, Raja; O'Donovan, Claire; Redaschi, Nicole; Suzek, Baris

    2006-01-01

    The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics. The UniProt Knowledgebase (UniProtKB), comprising the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniProtKB/TrEMBL section, is the preeminent storehouse of protein annotation. The extensive cross-references, functional and feature annotations and literature-based evidence attribution enable scientists to analyse proteins and query across databases. The UniProt Reference Clusters (UniRef) speed similarity searches via sequence space compression by merging sequences that are 100% (UniRef100), 90% (UniRef90) or 50% (UniRef50) identical. Finally, the UniProt Archive (UniParc) stores all publicly available protein sequences, containing the history of sequence data with links to the source databases. UniProt databases continue to grow in size and in availability of information. Recent and upcoming changes to database contents, formats, controlled vocabularies and services are described. New download availability includes all major releases of UniProtKB, sequence collections by taxonomic division and complete proteomes. A bibliography mapping service has been added, and an ID mapping service will be available soon. UniProt databases can be accessed online at or downloaded at . PMID:16381842

  4. Genes and proteins of Escherichia coli (GenProtEc).

    PubMed

    Riley, M; Space, D B

    1996-01-01

    GenProtEc is a database of Escherichia coli genes and their gene products, classified by type of function and physiological role and with citations to the literature for each. Also present are data on sequence similarities among E.coli proteins with PAM values, percent identity of amino acids, length of alignment and percent aligned. The database is available as a PKZip file by ftp from mbl.edu/pub/ecoli.exe. The program runs under MS-DOS on IMB-compatible machines. GenProtEc can also be accessed through the World Wide Web at URL http://mbl.edu/html/ecoli.html. PMID:8594596

  5. Radiation

    NASA Video Gallery

    Outside the protective cocoon of Earth's atmosphere, the universe is full of harmful radiation. Astronauts who live and work in space are exposed not only to ultraviolet rays but also to space radi...

  6. 49 CFR Appendix D to Part 26 - Mentor-Protégé Program Guidelines

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 1 2011-10-01 2011-10-01 false Mentor-Protégé Program Guidelines D Appendix D... D to Part 26—Mentor-Protégé Program Guidelines (A) The purpose of this program element is to further... and assistance from other firms. To operate a mentor-protégé program, a recipient must obtain...

  7. 49 CFR Appendix D to Part 26 - Mentor-Protégé Program Guidelines

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 1 2014-10-01 2014-10-01 false Mentor-Protégé Program Guidelines D Appendix D... D to Part 26—Mentor-Protégé Program Guidelines (A) The purpose of this program element is to further... and assistance from other firms. To operate a mentor-protégé program, a recipient must obtain...

  8. 48 CFR 852.219-71 - VA mentor-protégé program.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 5 2011-10-01 2011-10-01 false VA mentor-protégÃ....219-71 VA mentor-protégé program. As prescribed in 819.7115(a), insert the following clause: VA Mentor-Protégé Program (DEC 2009) (a) Large businesses are encouraged to participate in the VA...

  9. 48 CFR 852.219-71 - VA mentor-protégé program.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 5 2012-10-01 2012-10-01 false VA mentor-protégÃ....219-71 VA mentor-protégé program. As prescribed in 819.7115(a), insert the following clause: VA Mentor-Protégé Program (DEC 2009) (a) Large businesses are encouraged to participate in the VA...

  10. 48 CFR 852.219-71 - VA mentor-protégé program.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 5 2013-10-01 2013-10-01 false VA mentor-protégÃ....219-71 VA mentor-protégé program. As prescribed in 819.7115(a), insert the following clause: VA Mentor-Protégé Program (DEC 2009) (a) Large businesses are encouraged to participate in the VA...

  11. 48 CFR 752.219-70 - USAID Mentor-Protégé Program.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... developmental assistance. Protégé firms are small business as defined in 13 CFR parts 121, 124, and 126. (c... 48 Federal Acquisition Regulations System 5 2011-10-01 2011-10-01 false USAID Mentor-ProtégÃ....219-70 USAID Mentor-Protégé Program. As prescribed in 719.273-11(a), insert the following...

  12. 48 CFR 752.219-70 - USAID Mentor-Protégé Program.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... developmental assistance. Protégé firms are small business as defined in 13 CFR parts 121, 124, and 126. (c... 48 Federal Acquisition Regulations System 5 2012-10-01 2012-10-01 false USAID Mentor-ProtégÃ....219-70 USAID Mentor-Protégé Program. As prescribed in 719.273-11(a), insert the following...

  13. 48 CFR 852.219-71 - VA mentor-protégé program.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false VA mentor-protégÃ....219-71 VA mentor-protégé program. As prescribed in 819.7115(a), insert the following clause: VA Mentor-Protégé Program (DEC 2009) (a) Large businesses are encouraged to participate in the VA...

  14. 48 CFR 752.219-70 - USAID Mentor-Protégé Program.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... developmental assistance. Protégé firms are small business as defined in 13 CFR parts 121, 124, and 126. (c... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false USAID Mentor-ProtégÃ....219-70 USAID Mentor-Protégé Program. As prescribed in 719.273-11(a), insert the following...

  15. 48 CFR 752.219-70 - USAID Mentor-Protégé Program.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... developmental assistance. Protégé firms are small business as defined in 13 CFR parts 121, 124, and 126. (c... 48 Federal Acquisition Regulations System 5 2014-10-01 2014-10-01 false USAID Mentor-ProtégÃ....219-70 USAID Mentor-Protégé Program. As prescribed in 719.273-11(a), insert the following...

  16. 49 CFR Appendix D to Part 26 - Mentor-Protégé Program Guidelines

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 1 2010-10-01 2010-10-01 false Mentor-Protégé Program Guidelines D Appendix D... D to Part 26—Mentor-Protégé Program Guidelines (A) The purpose of this program element is to further... and assistance from other firms. To operate a mentor-protégé program, a recipient must obtain...

  17. 48 CFR 852.219-71 - VA mentor-protégé program.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 5 2014-10-01 2014-10-01 false VA mentor-protégÃ....219-71 VA mentor-protégé program. As prescribed in 819.7115(a), insert the following clause: VA Mentor-Protégé Program (DEC 2009) (a) Large businesses are encouraged to participate in the VA...

  18. 48 CFR 752.219-70 - USAID Mentor-Protégé Program.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... developmental assistance. Protégé firms are small business as defined in 13 CFR parts 121, 124, and 126. (c... 48 Federal Acquisition Regulations System 5 2013-10-01 2013-10-01 false USAID Mentor-ProtégÃ....219-70 USAID Mentor-Protégé Program. As prescribed in 719.273-11(a), insert the following...

  19. LassoProt: server to analyze biopolymers with lassos

    PubMed Central

    Dabrowski-Tumanski, Pawel; Niemyska, Wanda; Pasznik, Pawel; Sulkowska, Joanna I.

    2016-01-01

    The LassoProt server, http://lassoprot.cent.uw.edu.pl/, enables analysis of biopolymers with entangled configurations called lassos. The server offers various ways of visualizing lasso configurations, as well as their time trajectories, with all the results and plots downloadable. Broad spectrum of applications makes LassoProt a useful tool for biologists, biophysicists, chemists, polymer physicists and mathematicians. The server and our methods have been validated on the whole PDB, and the results constitute the database of proteins with complex lassos, supported with basic biological data. This database can serve as a source of information about protein geometry and entanglement-function correlations, as a reference set in protein modeling, and for many other purposes. PMID:27131383

  20. Automated annotation of microbial proteomes in SWISS-PROT.

    PubMed

    Gattiker, Alexandre; Michoud, Karine; Rivoire, Catherine; Auchincloss, Andrea H; Coudert, Elisabeth; Lima, Tania; Kersey, Paul; Pagni, Marco; Sigrist, Christian J A; Lachaize, Corinne; Veuthey, Anne Lise; Gasteiger, Elisabeth; Bairoch, Amos

    2003-02-01

    Large-scale sequencing of prokaryotic genomes demands the automation of certain annotation tasks currently manually performed in the production of the SWISS-PROT protein knowledgebase. The HAMAP project, or 'High-quality Automated and Manual Annotation of microbial Proteomes', aims to integrate manual and automatic annotation methods in order to enhance the speed of the curation process while preserving the quality of the database annotation. Automatic annotation is only applied to entries that belong to manually defined orthologous families and to entries with no identifiable similarities (ORFans). Many checks are enforced in order to prevent the propagation of wrong annotation and to spot problematic cases, which are channelled to manual curation. The results of this annotation are integrated in SWISS-PROT, and a website is provided at http://www.expasy.org/sprot/hamap/. PMID:12798039

  1. LassoProt: server to analyze biopolymers with lassos.

    PubMed

    Dabrowski-Tumanski, Pawel; Niemyska, Wanda; Pasznik, Pawel; Sulkowska, Joanna I

    2016-07-01

    The LassoProt server, http://lassoprot.cent.uw.edu.pl/, enables analysis of biopolymers with entangled configurations called lassos. The server offers various ways of visualizing lasso configurations, as well as their time trajectories, with all the results and plots downloadable. Broad spectrum of applications makes LassoProt a useful tool for biologists, biophysicists, chemists, polymer physicists and mathematicians. The server and our methods have been validated on the whole PDB, and the results constitute the database of proteins with complex lassos, supported with basic biological data. This database can serve as a source of information about protein geometry and entanglement-function correlations, as a reference set in protein modeling, and for many other purposes. PMID:27131383

  2. Swiss-Prot: juggling between evolution and stability.

    PubMed

    Bairoch, Amos; Boeckmann, Brigitte; Ferro, Serenella; Gasteiger, Elisabeth

    2004-03-01

    We describe some of the aspects of Swiss-Prot that make it unique, explain what are the developments we believe to be necessary for the database to continue to play its role as a focal point of protein knowledge, and provide advice pertinent to the development of high-quality knowledge resources on one aspect or the other of the life sciences. PMID:15153305

  3. Analysis of the tryptic search space in UniProt databases

    PubMed Central

    Alpi, Emanuele; Griss, Johannes; da Silva, Alan Wilter Sousa; Bely, Benoit; Antunes, Ricardo; Zellner, Hermann; Ríos, Daniel; O'Donovan, Claire; Vizcaíno, Juan Antonio; Martin, Maria J

    2015-01-01

    In this article, we provide a comprehensive study of the content of the Universal Protein Resource (UniProt) protein data sets for human and mouse. The tryptic search spaces of the UniProtKB (UniProt knowledgebase) complete proteome sets were compared with other data sets from UniProtKB and with the corresponding International Protein Index, reference sequence, Ensembl, and UniRef100 (where UniRef is UniProt reference clusters) organism-specific data sets. All protein forms annotated in UniProtKB (both the canonical sequences and isoforms) were evaluated in this study. In addition, natural and disease-associated amino acid variants annotated in UniProtKB were included in the evaluation. The peptide unicity was also evaluated for each data set. Furthermore, the peptide information in the UniProtKB data sets was also compared against the available peptide-level identifications in the main MS-based proteomics repositories. Identifying the peptides observed in these repositories is an important resource of information for protein databases as they provide supporting evidence for the existence of otherwise predicted proteins. Likewise, the repositories could use the information available in UniProtKB to direct reprocessing efforts on specific sets of peptides/proteins of interest. In summary, we provide comprehensive information about the different organism-specific sequence data sets available from UniProt, together with the pros and cons for each, in terms of search space for MS-based bottom-up proteomics workflows. The aim of the analysis is to provide a clear view of the tryptic search space of UniProt and other protein databases to enable scientists to select those most appropriate for their purposes. PMID:25307260

  4. MultitaskProtDB: a database of multitasking proteins.

    PubMed

    Hernández, Sergio; Ferragut, Gabriela; Amela, Isaac; Perez-Pons, JosepAntoni; Piñol, Jaume; Mozo-Villarias, Angel; Cedano, Juan; Querol, Enrique

    2014-01-01

    We have compiled MultitaskProtDB, available online at http://wallace.uab.es/multitask, to provide a repository where the many multitasking proteins found in the literature can be stored. Multitasking or moonlighting is the capability of some proteins to execute two or more biological functions. Usually, multitasking proteins are experimentally revealed by serendipity. This ability of proteins to perform multitasking functions helps us to understand one of the ways used by cells to perform many complex functions with a limited number of genes. Even so, the study of this phenomenon is complex because, among other things, there is no database of moonlighting proteins. The existence of such a tool facilitates the collection and dissemination of these important data. This work reports the database, MultitaskProtDB, which is designed as a friendly user web page containing >288 multitasking proteins with their NCBI and UniProt accession numbers, canonical and additional biological functions, monomeric/oligomeric states, PDB codes when available and bibliographic references. This database also serves to gain insight into some characteristics of multitasking proteins such as frequencies of the different pairs of functions, phylogenetic conservation and so forth. PMID:24253302

  5. A fast Peptide Match service for UniProt Knowledgebase

    PubMed Central

    Chen, Chuming; Li, Zhiwen; Huang, Hongzhan; Suzek, Baris E.; Wu, Cathy H.

    2013-01-01

    Summary: We have developed a new web application for peptide matching using Apache Lucene-based search engine. The Peptide Match service is designed to quickly retrieve all occurrences of a given query peptide from UniProt Knowledgebase (UniProtKB) with isoforms. The matched proteins are shown in summary tables with rich annotations, including matched sequence region(s) and links to corresponding proteins in a number of proteomic/peptide spectral databases. The results are grouped by taxonomy and can be browsed by organism, taxonomic group or taxonomy tree. The service supports queries where isobaric leucine and isoleucine are treated equivalent, and an option for searching UniRef100 representative sequences, as well as dynamic queries to major proteomic databases. In addition to the web interface, we also provide RESTful web services. The underlying data are updated every 4 weeks in accordance with the UniProt releases. Availability: http://proteininformationresource.org/peptide.shtml Contact: chenc@udel.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23958731

  6. 76 FR 70828 - Proposed Information Collection (Mentor-Protégé Program Application and Reports) Activity...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-15

    ... AFFAIRS Proposed Information Collection (Mentor-Prot g Program Application and Reports) Activity; Comment... needed to establish a mentor-prot g program agreement between a large business, veteran-owned small... will be used to institute a mentor-prot g program whereby large businesses agree to provide...

  7. 48 CFR 1019.202-70-8 - Protégé firms.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS Policies 1019.202-70-8 Protégé firms. (a) For selection as a protégé, a firm must be: (1) A small business, women-owned small business, small disadvantaged business, small business owned and controlled by service disabled veterans, or qualified HUBZone small......

  8. 48 CFR 3052.219-71 - DHS mentor-protégé program.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... CONTRACT CLAUSES Text of Provisions and Clauses 3052.219-71 DHS mentor-protégé program. As prescribed in (HSAR) 48 CFR 3019.708-70(b), insert the following clause: DHS Mentor-Protégé Program (JUN 2006) (a... 48 Federal Acquisition Regulations System 7 2010-10-01 2010-10-01 false DHS...

  9. 48 CFR 519.7007 - Protégé firms.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... disadvantaged business status eligibility and documentation requirements are determined according to 13 CFR... PROGRAMS SMALL BUSINESS PROGRAMS GSA Mentor-Protégé Program 519.7007 Protégé firms. (a) For selection as.../mentor assigns to the subcontract; and (3) Eligible (not listed in the “Excluded Parties List...

  10. 48 CFR 719.273-4 - Eligibility of Mentor and Protégé firms.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... documentation requirements are determined according to 13 CFR part 124. ... 48 Federal Acquisition Regulations System 5 2012-10-01 2012-10-01 false Eligibility of Mentor and... Development (USAID) Mentor-Protégé Program 719.273-4 Eligibility of Mentor and Protégé firms....

  11. 48 CFR 3052.219-71 - DHS mentor-protégé program.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... CONTRACT CLAUSES Text of Provisions and Clauses 3052.219-71 DHS mentor-protégé program. As prescribed in (HSAR) 48 CFR 3019.708-70(b), insert the following clause: DHS Mentor-Protégé Program (JUN 2006) (a... 48 Federal Acquisition Regulations System 7 2012-10-01 2012-10-01 false DHS...

  12. 48 CFR 3052.219-71 - DHS mentor-protégé program.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... CONTRACT CLAUSES Text of Provisions and Clauses 3052.219-71 DHS mentor-protégé program. As prescribed in (HSAR) 48 CFR 3019.708-70(b), insert the following clause: DHS Mentor-Protégé Program (JUN 2006) (a... 48 Federal Acquisition Regulations System 7 2014-10-01 2014-10-01 false DHS...

  13. 48 CFR 819.7106 - Eligibility of Mentor and Protégé firms.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 5 2012-10-01 2012-10-01 false Eligibility of Mentor and... VETERANS AFFAIRS SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS VA Mentor-Protégé Program 819.7106 Eligibility of Mentor and Protégé firms. Eligible business entities approved as mentors may enter...

  14. 48 CFR 519.7007 - Protégé firms.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... disadvantaged business status eligibility and documentation requirements are determined according to 13 CFR... PROGRAMS SMALL BUSINESS PROGRAMS GSA Mentor-Protégé Program 519.7007 Protégé firms. (a) For selection as.../mentor assigns to the subcontract; and (3) Eligible (not listed in the “Excluded Parties List...

  15. 48 CFR 719.273-4 - Eligibility of Mentor and Protégé firms.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... documentation requirements are determined according to 13 CFR part 124. ... 48 Federal Acquisition Regulations System 5 2013-10-01 2013-10-01 false Eligibility of Mentor and... Development (USAID) Mentor-Protégé Program 719.273-4 Eligibility of Mentor and Protégé firms....

  16. 48 CFR 519.7007 - Protégé firms.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... disadvantaged business status eligibility and documentation requirements are determined according to 13 CFR... PROGRAMS SMALL BUSINESS PROGRAMS GSA Mentor-Protégé Program 519.7007 Protégé firms. (a) For selection as.../mentor assigns to the subcontract; and (3) Eligible (not listed in the “Excluded Parties List...

  17. 48 CFR 819.7106 - Eligibility of Mentor and Protégé firms.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 5 2013-10-01 2013-10-01 false Eligibility of Mentor and... VETERANS AFFAIRS SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS VA Mentor-Protégé Program 819.7106 Eligibility of Mentor and Protégé firms. Eligible business entities approved as mentors may enter...

  18. 48 CFR 1019.202-70 - The Treasury Mentor Protégé Program.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 5 2012-10-01 2012-10-01 false The Treasury Mentor ProtÃ... THE TREASURY SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS Policies 1019.202-70 The Treasury Mentor... not be considered an affiliate of a mentor firm solely on the basis that the protégé firm is...

  19. 48 CFR 719.273-4 - Eligibility of Mentor and Protégé firms.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... documentation requirements are determined according to 13 CFR part 124. ... 48 Federal Acquisition Regulations System 5 2014-10-01 2014-10-01 false Eligibility of Mentor and... Development (USAID) Mentor-Protégé Program 719.273-4 Eligibility of Mentor and Protégé firms....

  20. 48 CFR 1019.202-70 - The Treasury Mentor Protégé Program.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 5 2014-10-01 2014-10-01 false The Treasury Mentor ProtÃ... THE TREASURY SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS Policies 1019.202-70 The Treasury Mentor... not be considered an affiliate of a mentor firm solely on the basis that the protégé firm is...

  1. 48 CFR 3052.219-71 - DHS mentor-protégé program.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... CONTRACT CLAUSES Text of Provisions and Clauses 3052.219-71 DHS mentor-protégé program. As prescribed in (HSAR) 48 CFR 3019.708-70(b), insert the following clause: DHS Mentor-Protégé Program (JUN 2006) (a... 48 Federal Acquisition Regulations System 7 2011-10-01 2011-10-01 false DHS...

  2. 48 CFR 3052.219-71 - DHS mentor-protégé program.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... CONTRACT CLAUSES Text of Provisions and Clauses 3052.219-71 DHS mentor-protégé program. As prescribed in (HSAR) 48 CFR 3019.708-70(b), insert the following clause: DHS Mentor-Protégé Program (JUN 2006) (a... 48 Federal Acquisition Regulations System 7 2013-10-01 2012-10-01 true DHS...

  3. 48 CFR 719.273-4 - Eligibility of Mentor and Protégé firms.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... documentation requirements are determined according to 13 CFR part 124. ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Eligibility of Mentor and... Development (USAID) Mentor-Protégé Program 719.273-4 Eligibility of Mentor and Protégé firms....

  4. 48 CFR 1019.202-70 - The Treasury Mentor Protégé Program.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 5 2013-10-01 2013-10-01 false The Treasury Mentor ProtÃ... THE TREASURY SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS Policies 1019.202-70 The Treasury Mentor... not be considered an affiliate of a mentor firm solely on the basis that the protégé firm is...

  5. 48 CFR 819.7106 - Eligibility of Mentor and Protégé firms.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 5 2011-10-01 2011-10-01 false Eligibility of Mentor and... VETERANS AFFAIRS SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS VA Mentor-Protégé Program 819.7106 Eligibility of Mentor and Protégé firms. Eligible business entities approved as mentors may enter...

  6. 48 CFR 519.7007 - Protégé firms.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... disadvantaged business status eligibility and documentation requirements are determined according to 13 CFR... PROGRAMS SMALL BUSINESS PROGRAMS GSA Mentor-Protégé Program 519.7007 Protégé firms. (a) For selection as.../mentor assigns to the subcontract; and (3) Eligible (not listed in the “Excluded Parties List...

  7. 48 CFR 819.7106 - Eligibility of Mentor and Protégé firms.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 5 2014-10-01 2014-10-01 false Eligibility of Mentor and... VETERANS AFFAIRS SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS VA Mentor-Protégé Program 819.7106 Eligibility of Mentor and Protégé firms. Eligible business entities approved as mentors may enter...

  8. 48 CFR 519.7007 - Protégé firms.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... disadvantaged business status eligibility and documentation requirements are determined according to 13 CFR... PROGRAMS SMALL BUSINESS PROGRAMS GSA Mentor-Protégé Program 519.7007 Protégé firms. (a) For selection as.../mentor assigns to the subcontract; and (3) Eligible (not listed in the “Excluded Parties List...

  9. 48 CFR 719.273-4 - Eligibility of Mentor and Protégé firms.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... documentation requirements are determined according to 13 CFR part 124. ... 48 Federal Acquisition Regulations System 5 2011-10-01 2011-10-01 false Eligibility of Mentor and... Development (USAID) Mentor-Protégé Program 719.273-4 Eligibility of Mentor and Protégé firms....

  10. 48 CFR 1852.219-77 - NASA Mentor-Protégé Program.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... companies or nonprofit agencies employing people who are blind or severely disabled as defined in 41 CFR... 48 Federal Acquisition Regulations System 6 2014-10-01 2014-10-01 false NASA Mentor-ProtégÃ... and Clauses 1852.219-77 NASA Mentor-Protégé Program. As prescribed in 1819.7215, insert the...

  11. 48 CFR 1852.219-77 - NASA Mentor-Protégé Program.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... companies or nonprofit agencies employing people who are blind or severely disabled as defined in 41 CFR... 48 Federal Acquisition Regulations System 6 2011-10-01 2011-10-01 false NASA Mentor-ProtégÃ... and Clauses 1852.219-77 NASA Mentor-Protégé Program. As prescribed in 1819.7215, insert the...

  12. 48 CFR 1852.219-77 - NASA Mentor-Protégé Program.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... companies or nonprofit agencies employing people who are blind or severely disabled as defined in 41 CFR... 48 Federal Acquisition Regulations System 6 2012-10-01 2012-10-01 false NASA Mentor-ProtégÃ... and Clauses 1852.219-77 NASA Mentor-Protégé Program. As prescribed in 1819.7215, insert the...

  13. 48 CFR 1852.219-77 - NASA Mentor-Protégé Program.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... companies or nonprofit agencies employing people who are blind or severely disabled as defined in 41 CFR... 48 Federal Acquisition Regulations System 6 2013-10-01 2013-10-01 false NASA Mentor-ProtégÃ... and Clauses 1852.219-77 NASA Mentor-Protégé Program. As prescribed in 1819.7215, insert the...

  14. 48 CFR 1852.219-77 - NASA Mentor-Protégé Program.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... nonprofit agencies employing people who are blind or severely disabled as defined in 41 CFR Chapter 51. (3... 48 Federal Acquisition Regulations System 6 2010-10-01 2010-10-01 true NASA Mentor-ProtégÃ... and Clauses 1852.219-77 NASA Mentor-Protégé Program. As prescribed in 1819.7215, insert the...

  15. 49 CFR Appendix D to Part 26 - Mentor-Protégé Program Guidelines

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 1 2012-10-01 2012-10-01 false Mentor-Protégé Program Guidelines D Appendix D... BUSINESS ENTERPRISES IN DEPARTMENT OF TRANSPORTATION FINANCIAL ASSISTANCE PROGRAMS Pt. 26, App. D Appendix D to Part 26—Mentor-Protégé Program Guidelines (A) The purpose of this program element is to...

  16. 49 CFR Appendix D to Part 26 - Mentor-Protégé Program Guidelines

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 1 2013-10-01 2013-10-01 false Mentor-Protégé Program Guidelines D Appendix D... BUSINESS ENTERPRISES IN DEPARTMENT OF TRANSPORTATION FINANCIAL ASSISTANCE PROGRAMS Pt. 26, App. D Appendix D to Part 26—Mentor-Protégé Program Guidelines (A) The purpose of this program element is to...

  17. The Effect of Mentoring on Protégés' Organizational Deviance.

    PubMed

    Chen, Cheng; Wen, Peng

    2016-08-01

    The aim of the present study was to investigate the effect of mentoring on protégés' organizational deviance. The sample comprised 202 ongoing formal mentoring dyads in the People's Republic of China (mentor samples: 61.9% male, M age = 36.8 years; protégé samples: 57.4% male, M age = 25.0 years). The regression results showed that mentoring was negatively related to protégés' organizational deviance. Moreover, job embeddedness and organizational identification mediated the association between mentoring and protégés' organizational deviance. Furthermore, the perceived developmental climate played a significant moderating role in the relationships between mentoring and job embeddedness and organizational identification such that the relationships were stronger when protégés perceived a stronger developmental climate. The theoretical and practical implications of this study were discussed. PMID:27444657

  18. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999.

    PubMed Central

    Bairoch, A; Apweiler, R

    1999-01-01

    SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. Recent developments of the database include: cross-references to additional databases; a variety of new documentation files and improvements to TrEMBL, a computer annotated supplement to SWISS-PROT. TrEMBL consists of entries in SWISS-PROT-like format derived from the translation of all coding sequences (CDS) in the EMBL nucleotide sequence database, except the CDS already included in SWISS-PROT. The URLs for SWISS-PROT on the WWW are: http://www.expasy.ch/sprot and http://www. ebi.ac.uk/sprot PMID:9847139

  19. enDNA-Prot: Identification of DNA-Binding Proteins by Applying Ensemble Learning

    PubMed Central

    Xu, Ruifeng; Zhou, Jiyun; Liu, Bin; Yao, Lin; He, Yulan; Zou, Quan; Wang, Xiaolong

    2014-01-01

    DNA-binding proteins are crucial for various cellular processes, such as recognition of specific nucleotide, regulation of transcription, and regulation of gene expression. Developing an effective model for identifying DNA-binding proteins is an urgent research problem. Up to now, many methods have been proposed, but most of them focus on only one classifier and cannot make full use of the large number of negative samples to improve predicting performance. This study proposed a predictor called enDNA-Prot for DNA-binding protein identification by employing the ensemble learning technique. Experiential results showed that enDNA-Prot was comparable with DNA-Prot and outperformed DNAbinder and iDNA-Prot with performance improvement in the range of 3.97–9.52% in ACC and 0.08–0.19 in MCC. Furthermore, when the benchmark dataset was expanded with negative samples, the performance of enDNA-Prot outperformed the three existing methods by 2.83–16.63% in terms of ACC and 0.02–0.16 in terms of MCC. It indicated that enDNA-Prot is an effective method for DNA-binding protein identification and expanding training dataset with negative samples can improve its performance. For the convenience of the vast majority of experimental scientists, we developed a user-friendly web-server for enDNA-Prot which is freely accessible to the public. PMID:24977146

  20. newDNA-Prot: Prediction of DNA-binding proteins by employing support vector machine and a comprehensive sequence representation.

    PubMed

    Zhang, Yanping; Xu, Jun; Zheng, Wei; Zhang, Chen; Qiu, Xingye; Chen, Ke; Ruan, Jishou

    2014-10-01

    Identification of DNA-binding proteins is essential in studying cellular activities as the DNA-binding proteins play a pivotal role in gene regulation. In this study, we propose newDNA-Prot, a DNA-binding protein predictor that employs support vector machine classifier and a comprehensive feature representation. The sequence representation are categorized into 6 groups: primary sequence based, evolutionary profile based, predicted secondary structure based, predicted relative solvent accessibility based, physicochemical property based and biological function based features. The mRMR, wrapper and two-stage feature selection methods are employed for removing irrelevant features and reducing redundant features. Experiments demonstrate that the two-stage method performs better than the mRMR and wrapper methods. We also perform a statistical analysis on the selected features and results show that more than 95% of the selected features are statistically significant and they cover all 6 feature groups. The newDNA-Prot method is compared with several state of the art algorithms, including iDNA-Prot, DNAbinder and DNA-Prot. The results demonstrate that newDNA-Prot method outperforms the iDNA-Prot, DNAbinder and DNA-Prot methods. More specific, newDNA-Prot improves the runner-up method, DNA-Prot for around 10% on several evaluation measures. The proposed newDNA-Prot method is available at http://sourceforge.net/projects/newdnaprot/ PMID:25240115

  1. RaftProt: mammalian lipid raft proteome database

    PubMed Central

    Shah, Anup; Chen, David; Boda, Akash R.; Foster, Leonard J.; Davis, Melissa J.; Hill, Michelle M.

    2015-01-01

    RaftProt (http://lipid-raft-database.di.uq.edu.au/) is a database of mammalian lipid raft-associated proteins as reported in high-throughput mass spectrometry studies. Lipid rafts are specialized membrane microdomains enriched in cholesterol and sphingolipids thought to act as dynamic signalling and sorting platforms. Given their fundamental roles in cellular regulation, there is a plethora of information on the size, composition and regulation of these membrane microdomains, including a large number of proteomics studies. To facilitate the mining and analysis of published lipid raft proteomics studies, we have developed a searchable database RaftProt. In addition to browsing the studies, performing basic queries by protein and gene names, searching experiments by cell, tissue and organisms; we have implemented several advanced features to facilitate data mining. To address the issue of potential bias due to biochemical preparation procedures used, we have captured the lipid raft preparation methods and implemented advanced search option for methodology and sample treatment conditions, such as cholesterol depletion. Furthermore, we have identified a list of high confidence proteins, and enabled searching only from this list of likely bona fide lipid raft proteins. Given the apparent biological importance of lipid raft and their associated proteins, this database would constitute a key resource for the scientific community. PMID:25392410

  2. UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB

    PubMed Central

    Doğan, Tunca; MacDougall, Alistair; Saidi, Rabie; Poggioli, Diego; Bateman, Alex; O’Donovan, Claire; Martin, Maria J.

    2016-01-01

    Motivation: Similarity-based methods have been widely used in order to infer the properties of genes and gene products containing little or no experimental annotation. New approaches that overcome the limitations of methods that rely solely upon sequence similarity are attracting increased attention. One of these novel approaches is to use the organization of the structural domains in proteins. Results: We propose a method for the automatic annotation of protein sequences in the UniProt Knowledgebase (UniProtKB) by comparing their domain architectures, classifying proteins based on the similarities and propagating functional annotation. The performance of this method was measured through a cross-validation analysis using the Gene Ontology (GO) annotation of a sub-set of UniProtKB/Swiss-Prot. The results demonstrate the effectiveness of this approach in detecting functional similarity with an average F-score: 0.85. We applied the method on nearly 55.3 million uncharacterized proteins in UniProtKB/TrEMBL resulted in 44 818 178 GO term predictions for 12 172 114 proteins. 22% of these predictions were for 2 812 016 previously non-annotated protein entries indicating the significance of the value added by this approach. Availability and implementation: The results of the method are available at: ftp://ftp.ebi.ac.uk/pub/contrib/martin/DAAC/. Contact: tdogan@ebi.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153729

  3. The neXtProt knowledgebase on human proteins: current status

    PubMed Central

    Gaudet, Pascale; Michel, Pierre-André; Zahn-Zabal, Monique; Cusin, Isabelle; Duek, Paula D.; Evalet, Olivier; Gateau, Alain; Gleizes, Anne; Pereira, Mario; Teixeira, Daniel; Zhang, Ying; Lane, Lydie; Bairoch, Amos

    2015-01-01

    neXtProt (http://www.nextprot.org) is a human protein-centric knowledgebase developed at the SIB Swiss Institute of Bioinformatics. Focused solely on human proteins, neXtProt aims to provide a state of the art resource for the representation of human biology by capturing a wide range of data, precise annotations, fully traceable data provenance and a web interface which enables researchers to find and view information in a comprehensive manner. Since the introductory neXtProt publication, significant advances have been made on three main aspects: the representation of proteomics data, an extended representation of human variants and the development of an advanced search capability built around semantic technologies. These changes are presented in the current neXtProt update. PMID:25593349

  4. The SWISS-PROT protein sequence data bank and its new supplement TREMBL.

    PubMed Central

    Bairoch, A; Apweiler, R

    1996-01-01

    SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc), a minimal level of redundancy and a high level of integration with other databases. Recent developments of the database include: an increase in the number and scope of model organisms; cross-references to seven additional databases; a variety of new documentation files; the creation of TREMBL, and unannotated supplement to SWISS-PROT. This supplement consists of entries in SWISS-PROT-like format derived from the translation of all coding sequences (CDS) in the EMBL nucleotide sequence database, except CDS already included in SWISS-PROT. PMID:8594581

  5. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998.

    PubMed Central

    Bairoch, A; Apweiler, R

    1998-01-01

    SWISS-PROT (http://www.expasy.ch/) is a curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. Recent developments of the database include: an increase in the number and scope of model organisms; cross-references to two additional databases; a variety of new documentation files and improvements to TrEMBL, a computer annotated supplement to SWISS-PROT. TrEMBL consists of entries in SWISS-PROT-like format derived from the translation of all coding sequences (CDS) in the EMBL nucleotide sequence database, except the CDS already included in SWISS-PROT. PMID:9399796

  6. The neXtProt knowledgebase on human proteins: current status.

    PubMed

    Gaudet, Pascale; Michel, Pierre-André; Zahn-Zabal, Monique; Cusin, Isabelle; Duek, Paula D; Evalet, Olivier; Gateau, Alain; Gleizes, Anne; Pereira, Mario; Teixeira, Daniel; Zhang, Ying; Lane, Lydie; Bairoch, Amos

    2015-01-01

    neXtProt (http://www.nextprot.org) is a human protein-centric knowledgebase developed at the SIB Swiss Institute of Bioinformatics. Focused solely on human proteins, neXtProt aims to provide a state of the art resource for the representation of human biology by capturing a wide range of data, precise annotations, fully traceable data provenance and a web interface which enables researchers to find and view information in a comprehensive manner. Since the introductory neXtProt publication, significant advances have been made on three main aspects: the representation of proteomics data, an extended representation of human variants and the development of an advanced search capability built around semantic technologies. These changes are presented in the current neXtProt update. PMID:25593349

  7. The SWISS-PROT protein sequence data bank and its supplement TrEMBL.

    PubMed Central

    Bairoch, A; Apweiler, R

    1997-01-01

    SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, structure of its domains, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. Recent developments of the database include: an increase in the number and scope of model organisms; cross-references to two additional databases; a variety of new documentation files and the creation of TrEMBL, a computer annotated supplement to SWISS-PROT. This supplement consists of entries in SWISS-PROT-like format derived from the translation of all coding sequences (CDS) in the EMBL nucleotide sequence database, except the CDS already included in SWISS-PROT. PMID:9016499

  8. Representation of functional information in the SWISS-PROT data bank.

    PubMed

    Junker, V L; Apweiler, R; Bairoch, A

    1999-12-01

    Functional information in SWISS-PROT results, primarily, from assessment of articles reporting characterization. Predicted information is labeled with flags describing the evidence level (e.g. potential, probable, by similarity). PMID:10746001

  9. 48 CFR 1819.7205 - Mentor-protégé agreements.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ...-Commercial Items. (4) Loans. (5) Investment(s) in the protégé in exchange for an ownership interest in the... or all of the following types of developmental assistance: (1) Assistance by the mentor's...

  10. Genes and proteins of Escherichia coli K-12 (GenProtEC).

    PubMed

    Riley, M

    1997-01-01

    GenProtEC is a database of Escherichia coli genes and their gene products, classified by type of function and physiological role and with citations to the literature for each. Also present are data on sequence similarities amongE.coliproteins with PAM values, percent identity of amino acids, length of alignment and percent aligned. GenProtEC can also be accessed through the World Wide Web at URL http://mbl.edu/html/ecoli.html . PMID:9016503

  11. 48 CFR 852.219-72 - Evaluation factor for participation in the VA mentor-protégé program.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... participation in the VA mentor-protégé program. 852.219-72 Section 852.219-72 Federal Acquisition Regulations... Texts of Provisions and Clauses 852.219-72 Evaluation factor for participation in the VA mentor-protégé... the VA Mentor-Protégé Program (DEC2009) This solicitation contains an evaluation factor or...

  12. 48 CFR 619.202-70 - The Department of State Mentor-Protégé Program.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... Mentor-Protégé Program. 619.202-70 Section 619.202-70 Federal Acquisition Regulations System DEPARTMENT... Mentor-Protégé Program. (a) Purpose. The Mentor-Protégé Program is designed to motivate and encourage... service-disabled veteran-owned small business (SDVOSB) are the same as found in FAR 2.101. Mentor means...

  13. 48 CFR 852.219-72 - Evaluation factor for participation in the VA mentor-protégé program.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... participation in the VA mentor-protégé program. 852.219-72 Section 852.219-72 Federal Acquisition Regulations... Texts of Provisions and Clauses 852.219-72 Evaluation factor for participation in the VA mentor-protégé... the VA Mentor-Protégé Program (DEC2009) This solicitation contains an evaluation factor or...

  14. 48 CFR 619.202-70 - The Department of State Mentor-Protégé Program.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... Mentor-Protégé Program. 619.202-70 Section 619.202-70 Federal Acquisition Regulations System DEPARTMENT... Mentor-Protégé Program. (a) Purpose. The Mentor-Protégé Program is designed to motivate and encourage... service-disabled veteran-owned small business (SDVOSB) are the same as found in FAR 2.101. Mentor means...

  15. 48 CFR 852.219-72 - Evaluation factor for participation in the VA mentor-protégé program.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... participation in the VA mentor-protégé program. 852.219-72 Section 852.219-72 Federal Acquisition Regulations... Texts of Provisions and Clauses 852.219-72 Evaluation factor for participation in the VA mentor-protégé... the VA Mentor-Protégé Program (DEC2009) This solicitation contains an evaluation factor or...

  16. 48 CFR 619.202-70 - The Department of State Mentor-Protégé Program.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... Mentor-Protégé Program. 619.202-70 Section 619.202-70 Federal Acquisition Regulations System DEPARTMENT... Mentor-Protégé Program. (a) Purpose. The Mentor-Protégé Program is designed to motivate and encourage... service-disabled veteran-owned small business (SDVOSB) are the same as found in FAR 2.101. Mentor means...

  17. 48 CFR 852.219-72 - Evaluation factor for participation in the VA mentor-protégé program.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... participation in the VA mentor-protégé program. 852.219-72 Section 852.219-72 Federal Acquisition Regulations... Texts of Provisions and Clauses 852.219-72 Evaluation factor for participation in the VA mentor-protégé... the VA Mentor-Protégé Program (DEC2009) This solicitation contains an evaluation factor or...

  18. 48 CFR 852.219-72 - Evaluation factor for participation in the VA mentor-protégé program.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... participation in the VA mentor-protégé program. 852.219-72 Section 852.219-72 Federal Acquisition Regulations... Texts of Provisions and Clauses 852.219-72 Evaluation factor for participation in the VA mentor-protégé... the VA Mentor-Protégé Program (DEC2009) This solicitation contains an evaluation factor or...

  19. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000

    PubMed Central

    Bairoch, Amos; Apweiler, Rolf

    2000-01-01

    SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. Recent developments of the database include format and content enhancements, cross-references to additional databases, new documentation files and improvements to TrEMBL, a computer-annotated supplement to SWISS-PROT. TrEMBL consists of entries in SWISS-PROT-like format derived from the translation of all coding sequences (CDSs) in the EMBL Nucleotide Sequence Database, except the CDSs already included in SWISS-PROT. We also describe the Human Proteomics Initiative (HPI), a major project to annotate all known human sequences according to the quality standards of SWISS-PROT. SWISS-PROT is available at: http://www.expasy.ch/sprot/ and http://www.ebi.ac.uk/swissprot/ PMID:10592178

  20. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.

    PubMed

    Boeckmann, Brigitte; Bairoch, Amos; Apweiler, Rolf; Blatter, Marie-Claude; Estreicher, Anne; Gasteiger, Elisabeth; Martin, Maria J; Michoud, Karine; O'Donovan, Claire; Phan, Isabelle; Pilbout, Sandrine; Schneider, Michel

    2003-01-01

    The SWISS-PROT protein knowledgebase (http://www.expasy.org/sprot/ and http://www.ebi.ac.uk/swissprot/) connects amino acid sequences with the current knowledge in the Life Sciences. Each protein entry provides an interdisciplinary overview of relevant information by bringing together experimental results, computed features and sometimes even contradictory conclusions. Detailed expertise that goes beyond the scope of SWISS-PROT is made available via direct links to specialised databases. SWISS-PROT provides annotated entries for all species, but concentrates on the annotation of entries from human (the HPI project) and other model organisms to ensure the presence of high quality annotation for representative members of all protein families. Part of the annotation can be transferred to other family members, as is already done for microbes by the High-quality Automated and Manual Annotation of microbial Proteomes (HAMAP) project. Protein families and groups of proteins are regularly reviewed to keep up with current scientific findings. Complementarily, TrEMBL strives to comprise all protein sequences that are not yet represented in SWISS-PROT, by incorporating a perpetually increasing level of mostly automated annotation. Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to SWISS-PROT at swiss-prot@expasy.org. PMID:12520024

  1. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

    PubMed

    Bairoch, A; Apweiler, R

    2000-01-01

    SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. Recent developments of the database include format and content enhancements, cross-references to additional databases, new documentation files and improvements to TrEMBL, a computer-annotated supplement to SWISS-PROT. TrEMBL consists of entries in SWISS-PROT-like format derived from the translation of all coding sequences (CDSs) in the EMBL Nucleotide Sequence Database, except the CDSs already included in SWISS-PROT. We also describe the Human Proteomics Initiative (HPI), a major project to annotate all known human sequences according to the quality standards of SWISS-PROT. SWISS-PROT is available at: http://www.expasy.ch/sprot/ and http://www.ebi.ac.uk/swissprot/ PMID:10592178

  2. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

    PubMed Central

    Boeckmann, Brigitte; Bairoch, Amos; Apweiler, Rolf; Blatter, Marie-Claude; Estreicher, Anne; Gasteiger, Elisabeth; Martin, Maria J.; Michoud, Karine; O'Donovan, Claire; Phan, Isabelle; Pilbout, Sandrine; Schneider, Michel

    2003-01-01

    The SWISS-PROT protein knowledgebase (http://www.expasy.org/sprot/ and http://www.ebi.ac.uk/swissprot/) connects amino acid sequences with the current knowledge in the Life Sciences. Each protein entry provides an interdisciplinary overview of relevant information by bringing together experimental results, computed features and sometimes even contradictory conclusions. Detailed expertise that goes beyond the scope of SWISS-PROT is made available via direct links to specialised databases. SWISS-PROT provides annotated entries for all species, but concentrates on the annotation of entries from human (the HPI project) and other model organisms to ensure the presence of high quality annotation for representative members of all protein families. Part of the annotation can be transferred to other family members, as is already done for microbes by the High-quality Automated and Manual Annotation of microbial Proteomes (HAMAP) project. Protein families and groups of proteins are regularly reviewed to keep up with current scientific findings. Complementarily, TrEMBL strives to comprise all protein sequences that are not yet represented in SWISS-PROT, by incorporating a perpetually increasing level of mostly automated annotation. Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to SWISS-PROT at swiss-prot@expasy.org. PMID:12520024

  3. iDNA-Prot: identification of DNA binding proteins using random forest with grey model.

    PubMed

    Lin, Wei-Zhong; Fang, Jian-An; Xiao, Xuan; Chou, Kuo-Chen

    2011-01-01

    DNA-binding proteins play crucial roles in various cellular processes. Developing high throughput tools for rapidly and effectively identifying DNA-binding proteins is one of the major challenges in the field of genome annotation. Although many efforts have been made in this regard, further effort is needed to enhance the prediction power. By incorporating the features into the general form of pseudo amino acid composition that were extracted from protein sequences via the "grey model" and by adopting the random forest operation engine, we proposed a new predictor, called iDNA-Prot, for identifying uncharacterized proteins as DNA-binding proteins or non-DNA binding proteins based on their amino acid sequences information alone. The overall success rate by iDNA-Prot was 83.96% that was obtained via jackknife tests on a newly constructed stringent benchmark dataset in which none of the proteins included has ≥25% pairwise sequence identity to any other in a same subset. In addition to achieving high success rate, the computational time for iDNA-Prot is remarkably shorter in comparison with the relevant existing predictors. Hence it is anticipated that iDNA-Prot may become a useful high throughput tool for large-scale analysis of DNA-binding proteins. As a user-friendly web-server, iDNA-Prot is freely accessible to the public at the web-site on http://icpr.jci.edu.cn/bioinfo/iDNA-Prot or http://www.jci-bioinfo.cn/iDNA-Prot. Moreover, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results. PMID:21935457

  4. 13 CFR 126.618 - How does a HUBZone SBC's participation in a Mentor-Protégé relationship affect its participation...

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... participation in a Mentor-Protégé relationship affect its participation in the HUBZone Program? 126.618... Assistance § 126.618 How does a HUBZone SBC's participation in a Mentor-Protégé relationship affect its participation in the HUBZone Program? (a) Qualified HUBZone SBCs may enter into Mentor-Protégé relationships...

  5. 48 CFR 719.273 - The U.S. Agency for International Development (USAID) Mentor-Protégé Program.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... International Development (USAID) Mentor-Protégé Program. 719.273 Section 719.273 Federal Acquisition.... Agency for International Development (USAID) Mentor-Protégé Program 719.273 The U.S. Agency for International Development (USAID) Mentor-Protégé Program....

  6. 48 CFR 719.273 - The U.S. Agency for International Development (USAID) Mentor-Protégé Program.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... International Development (USAID) Mentor-Protégé Program. 719.273 Section 719.273 Federal Acquisition.... Agency for International Development (USAID) Mentor-Protégé Program 719.273 The U.S. Agency for International Development (USAID) Mentor-Protégé Program....

  7. 48 CFR 719.273 - The U.S. Agency for International Development (USAID) Mentor-Protégé Program.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... International Development (USAID) Mentor-Protégé Program. 719.273 Section 719.273 Federal Acquisition.... Agency for International Development (USAID) Mentor-Protégé Program 719.273 The U.S. Agency for International Development (USAID) Mentor-Protégé Program....

  8. 13 CFR 126.618 - How does a HUBZone SBC's participation in a Mentor-Protégé relationship affect its participation...

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... participation in a Mentor-Protégé relationship affect its participation in the HUBZone Program? 126.618... Assistance § 126.618 How does a HUBZone SBC's participation in a Mentor-Protégé relationship affect its participation in the HUBZone Program? (a) Qualified HUBZone SBCs may enter into Mentor-Protégé relationships...

  9. 13 CFR 126.618 - How does a HUBZone SBC's participation in a Mentor-Protégé relationship affect its participation...

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... participation in a Mentor-Protégé relationship affect its participation in the HUBZone Program? 126.618... Assistance § 126.618 How does a HUBZone SBC's participation in a Mentor-Protégé relationship affect its participation in the HUBZone Program? (a) Qualified HUBZone SBCs may enter into Mentor-Protégé relationships...

  10. 48 CFR 719.273 - The U.S. Agency for International Development (USAID) Mentor-Protégé Program.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... International Development (USAID) Mentor-Protégé Program. 719.273 Section 719.273 Federal Acquisition.... Agency for International Development (USAID) Mentor-Protégé Program 719.273 The U.S. Agency for International Development (USAID) Mentor-Protégé Program....

  11. 13 CFR 126.618 - How does a HUBZone SBC's participation in a Mentor-Protégé relationship affect its participation...

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... participation in a Mentor-Protégé relationship affect its participation in the HUBZone Program? 126.618... Assistance § 126.618 How does a HUBZone SBC's participation in a Mentor-Protégé relationship affect its participation in the HUBZone Program? (a) Qualified HUBZone SBCs may enter into Mentor-Protégé relationships...

  12. 48 CFR 719.273 - The U.S. Agency for International Development (USAID) Mentor-Protégé Program.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... International Development (USAID) Mentor-Protégé Program. 719.273 Section 719.273 Federal Acquisition.... Agency for International Development (USAID) Mentor-Protégé Program 719.273 The U.S. Agency for International Development (USAID) Mentor-Protégé Program....

  13. 13 CFR 126.618 - How does a HUBZone SBC's participation in a Mentor-Protégé relationship affect its participation...

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... participation in a Mentor-Protégé relationship affect its participation in the HUBZone Program? 126.618... Assistance § 126.618 How does a HUBZone SBC's participation in a Mentor-Protégé relationship affect its participation in the HUBZone Program? (a) Qualified HUBZone SBCs may enter into Mentor-Protégé relationships...

  14. HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot

    PubMed Central

    Lima, Tania; Auchincloss, Andrea H.; Coudert, Elisabeth; Keller, Guillaume; Michoud, Karine; Rivoire, Catherine; Bulliard, Virginie; de Castro, Edouard; Lachaize, Corinne; Baratin, Delphine; Phan, Isabelle; Bougueleret, Lydie; Bairoch, Amos

    2009-01-01

    The growth in the number of completely sequenced microbial genomes (bacterial and archaeal) has generated a need for a procedure that provides UniProtKB/Swiss-Prot-quality annotation to as many protein sequences as possible. We have devised a semi-automated system, HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes), that uses manually built annotation templates for protein families to propagate annotation to all members of manually defined protein families, using very strict criteria. The HAMAP system is composed of two databases, the proteome database and the family database, and of an automatic annotation pipeline. The proteome database comprises biological and sequence information for each completely sequenced microbial proteome, and it offers several tools for CDS searches, BLAST options and retrieval of specific sets of proteins. The family database currently comprises more than 1500 manually curated protein families and their annotation templates that are used to annotate proteins that belong to one of the HAMAP families. On the HAMAP website, individual sequences as well as whole genomes can be scanned against all HAMAP families. The system provides warnings for the absence of conserved amino acid residues, unusual sequence length, etc. Thanks to the implementation of HAMAP, more than 200 000 microbial proteins have been fully annotated in UniProtKB/Swiss-Prot (HAMAP website: http://www.expasy.org/sprot/hamap). PMID:18849571

  15. HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot.

    PubMed

    Lima, Tania; Auchincloss, Andrea H; Coudert, Elisabeth; Keller, Guillaume; Michoud, Karine; Rivoire, Catherine; Bulliard, Virginie; de Castro, Edouard; Lachaize, Corinne; Baratin, Delphine; Phan, Isabelle; Bougueleret, Lydie; Bairoch, Amos

    2009-01-01

    The growth in the number of completely sequenced microbial genomes (bacterial and archaeal) has generated a need for a procedure that provides UniProtKB/Swiss-Prot-quality annotation to as many protein sequences as possible. We have devised a semi-automated system, HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes), that uses manually built annotation templates for protein families to propagate annotation to all members of manually defined protein families, using very strict criteria. The HAMAP system is composed of two databases, the proteome database and the family database, and of an automatic annotation pipeline. The proteome database comprises biological and sequence information for each completely sequenced microbial proteome, and it offers several tools for CDS searches, BLAST options and retrieval of specific sets of proteins. The family database currently comprises more than 1500 manually curated protein families and their annotation templates that are used to annotate proteins that belong to one of the HAMAP families. On the HAMAP website, individual sequences as well as whole genomes can be scanned against all HAMAP families. The system provides warnings for the absence of conserved amino acid residues, unusual sequence length, etc. Thanks to the implementation of HAMAP, more than 200,000 microbial proteins have been fully annotated in UniProtKB/Swiss-Prot (HAMAP website: http://www.expasy.org/sprot/hamap). PMID:18849571

  16. 48 CFR 1052.219-73 - Department of the Treasury Mentor-Protégé Program.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... businesses as defined in 13 CFR parts 121, 124, and 126. Developmental assistance includes technical... Mentor-Protégé Program. 1052.219-73 Section 1052.219-73 Federal Acquisition Regulations System... and Clauses 1052.219-73 Department of the Treasury Mentor-Protégé Program. As prescribed in...

  17. 48 CFR 1052.219-73 - Department of the Treasury Mentor-Protégé Program.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... businesses as defined in 13 CFR parts 121, 124, and 126. Developmental assistance includes technical... Mentor-Protégé Program. 1052.219-73 Section 1052.219-73 Federal Acquisition Regulations System... and Clauses 1052.219-73 Department of the Treasury Mentor-Protégé Program. As prescribed in...

  18. 48 CFR 1052.219-73 - Department of the Treasury Mentor-Protégé Program.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... businesses as defined in 13 CFR parts 121, 124, and 126. Developmental assistance includes technical... Mentor-Protégé Program. 1052.219-73 Section 1052.219-73 Federal Acquisition Regulations System... and Clauses 1052.219-73 Department of the Treasury Mentor-Protégé Program. As prescribed in...

  19. 77 FR 3842 - Agency Information Collection (Mentor-Protégé Program Application and Reports) Activities Under...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-25

    ... AFFAIRS Agency Information Collection (Mentor-Prot g Program Application and Reports) Activities Under OMB... Veterans Acquisition Regulation (VAAR) Clauses 819.7108 and 819.7113 will be used to institute a mentor... the specific actions taken by the mentor to increase the participation of the prot g as a prime...

  20. 48 CFR 1052.219-73 - Department of the Treasury Mentor-Protégé Program.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... businesses as defined in 13 CFR parts 121, 124, and 126. Developmental assistance includes technical... Mentor-Protégé Program. 1052.219-73 Section 1052.219-73 Federal Acquisition Regulations System... and Clauses 1052.219-73 Department of the Treasury Mentor-Protégé Program. As prescribed in...

  1. 48 CFR 1052.219-73 - Department of the Treasury Mentor-Protégé Program.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... as defined in 13 CFR parts 121, 124, and 126. Developmental assistance is technical, managerial... Mentor-Protégé Program. 1052.219-73 Section 1052.219-73 Federal Acquisition Regulations System... and Clauses 1052.219-73 Department of the Treasury Mentor-Protégé Program. As described in DTAR...

  2. Mentoring early-career preventionists: current views from mentors and protégés.

    PubMed

    Véronneau, Marie-Hélène; Cance, Jessica Duncan; Ridenour, Ty A

    2012-10-01

    In prevention science, much of the training occurs outside of a formal graduate program and mentorship is invaluable to early-career individuals. A sample of the Society for Prevention Research (SPR) membership (N = 97) from a wide range of career levels completed an online questionnaire in spring 2010. Almost 20% identified as mentors, 32% as protégés, and 49% as both a mentor and a protégé. Most mentoring relationships were established in graduate school, but professional organizations such as SPR facilitated nearly one in five mentoring relationships. Qualitative results suggested that participants value their professional organization's support of mentoring and would support initiatives to increase mentoring relationships specifically among SPR members. Although all mentor functions and protégé responsibilities were rated as important, professional support was the highest ranked mentor function and taking initiative the highest ranked protégé responsibility. Additionally, the qualitative results revealed that interpersonal skills and commitment to the mentoring process were seen as key to positive mentoring relationships. We also found that formal documentation of mentoring agreements was rare and a slight preference for a match on gender or ethnicity was observed for protégés from nondominant groups. The discussion includes implications for individuals and implications for promoting high-quality mentoring within professional organizations. PMID:22562694

  3. SWISS-PROT: connecting biomolecular knowledge via a protein database.

    PubMed

    Gasteiger, E; Jung, E; Bairoch, A

    2001-07-01

    With the explosive growth of biological data, the development of new means of data storage was needed. More and more often biological information is no longer published in the conventional way via a publication in a scientific journal, but only deposited into a database. In the last two decades these databases have become essential tools for researchers in biological sciences. Biological databases can be classified according to the type of information they contain. There are basically three types of sequence-related databases (nucleic acid sequences, protein sequences and protein tertiary structures) as well as various specialized data collections. It is important to provide the users of biomolecular databases with a degree of integration between these databases as by nature all of these databases are connected in a scientific sense and each one of them is an important piece to biological complexity. In this review we will highlight our effort in connecting biological information as demonstrated in the SWISS-PROT protein database. PMID:11488411

  4. Protégé: a tool for managing and using terminology in radiology applications.

    PubMed

    Rubin, Daniel L; Noy, Natalya F; Musen, Mark A

    2007-11-01

    The development of standard terminologies such as RadLex is becoming important in radiology applications, such as structured reporting, teaching file authoring, report indexing, and text mining. The development and maintenance of these terminologies are challenging, however, because there are few specialized tools to help developers to browse, visualize, and edit large taxonomies. Protégé ( http://protege.stanford.edu ) is an open-source tool that allows developers to create and to manage terminologies and ontologies. It is more than a terminology-editing tool, as it also provides a platform for developers to use the terminologies in end-user applications. There are more than 70,000 registered users of Protégé who are using the system to manage terminologies and ontologies in many different domains. The RadLex project has recently adopted Protégé for managing its radiology terminology. Protégé provides several features particularly useful to managing radiology terminologies: an intuitive graphical user interface for navigating large taxonomies, visualization components for viewing complex term relationships, and a programming interface so developers can create terminology-driven radiology applications. In addition, Protégé has an extensible plug-in architecture, and its large user community has contributed a rich library of components and extensions that provide much additional useful functionalities. In this report, we describe Protégé's features and its particular advantages in the radiology domain in the creation, maintenance, and use of radiology terminology. PMID:17687607

  5. Protéger les nourrissons contre la coqueluche

    PubMed Central

    Gilley, Meghan; Goldman, Ran D.

    2014-01-01

    Résumé Question Compte tenu du taux à la hausse de la coqueluche chez les enfants, plusieurs familles m’ont demandé quels moyens prendre pour protéger leurs tout-petits de cette infection. Quelles devraient être mes recommandations à ces familles? Réponse La coqueluche est une maladie évitable qui est endémique dans le monde entier. Chez les adultes, la coqueluche cause une maladie bénigne semblable à un rhume, suivie d’une toux persistante. Chez les nourrissons, elle peut causer de l’apnée, des convulsions, une encéphalopathie, une bronchopneumonie et la mort. Les décès dus à la coqueluche se produisent dans 86 % des cas chez des nourrissons de moins de 4 mois. La stratégie du cocooning, c’est-à-dire la vaccination des adultes en étroit contact avec des nourrissons, est recommandée par de nombreuses agences mondiales et nationales, mais elle ne prévient probablement que 20 % des cas de coqueluche chez les nourrissons. La vaccination durant la grossesse est plus efficace, mais elle n’est pas encore approuvée au Canada. Il n’a pas été démontré que la vaccination à la naissance soit uniformément efficace et elle n’est donc pas recommandée à l’heure actuelle.

  6. 48 CFR 652.219-72 - Department of State Mentor-Protégé Program.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 13 CFR parts 121, 124, and 126. (c) Developmental assistance is technical, managerial, financial, and... 48 Federal Acquisition Regulations System 4 2014-10-01 2014-10-01 false Department of State Mentor....219-72 Department of State Mentor-Protégé Program. As prescribed in 619.202-70(o)(1), insert...

  7. 48 CFR 652.219-72 - Department of State Mentor-Protégé Program.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 13 CFR parts 121, 124, and 126. (c) Developmental assistance is technical, managerial, financial, and... 48 Federal Acquisition Regulations System 4 2010-10-01 2010-10-01 false Department of State Mentor....219-72 Department of State Mentor-Protégé Program. As prescribed in 619.202-70(o)(1), insert...

  8. 48 CFR 652.219-72 - Department of State Mentor-Protégé Program.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 13 CFR parts 121, 124, and 126. (c) Developmental assistance is technical, managerial, financial, and... 48 Federal Acquisition Regulations System 4 2012-10-01 2012-10-01 false Department of State Mentor....219-72 Department of State Mentor-Protégé Program. As prescribed in 619.202-70(o)(1), insert...

  9. 48 CFR 652.219-72 - Department of State Mentor-Protégé Program.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 13 CFR parts 121, 124, and 126. (c) Developmental assistance is technical, managerial, financial, and... 48 Federal Acquisition Regulations System 4 2013-10-01 2013-10-01 false Department of State Mentor....219-72 Department of State Mentor-Protégé Program. As prescribed in 619.202-70(o)(1), insert...

  10. 48 CFR 652.219-72 - Department of State Mentor-Protégé Program.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 13 CFR parts 121, 124, and 126. (c) Developmental assistance is technical, managerial, financial, and... 48 Federal Acquisition Regulations System 4 2011-10-01 2011-10-01 false Department of State Mentor....219-72 Department of State Mentor-Protégé Program. As prescribed in 619.202-70(o)(1), insert...

  11. 48 CFR 1019.202-70 - The Treasury Mentor-Protégé Program.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false The Treasury Mentor-Protégé Program. 1019.202-70 Section 1019.202-70 Federal Acquisition Regulations System DEPARTMENT OF THE TREASURY SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS Policies 1019.202-70 The Treasury...

  12. 48 CFR 819.7106 - Eligibility of Mentor and Protégé firms.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Eligibility of Mentor and Protégé firms. 819.7106 Section 819.7106 Federal Acquisition Regulations System DEPARTMENT OF... addition to VA's Program should maintain a system for preparing separate reports of mentoring activity...

  13. ProGlycProt: a repository of experimentally characterized prokaryotic glycoproteins

    PubMed Central

    Bhat, Aadil H.; Mondal, Homchoru; Chauhan, Jagat S.; Raghava, Gajendra P. S.; Methi, Amrish; Rao, Alka

    2012-01-01

    ProGlycProt (http://www.proglycprot.org/) is an open access, manually curated, comprehensive repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). To facilitate maximum information at one point, the database is arranged under two sections: (i) ProCGP—the main data section consisting of 95 entries with experimentally characterized glycosites and (ii) ProUGP—a supplementary data section containing 245 entries with experimentally identified glycosylation but uncharacterized glycosites. Every entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information. Interestingly, ProGlycProt contains as many as 174 entries for which information is unavailable or the characterized glycosites are unannotated in Swiss-Prot release 2011_07. The website supports a dedicated structure gallery of homology models and crystal structures of characterized glycoproteins in addition to two new tools developed in view of emerging information about prokaryotic sequons (conserved sequences of amino acids around glycosites) that are never or rarely seen in eukaryotic glycoproteins. ProGlycProt provides an extensive compilation of experimentally identified glycosites (334) and glycoproteins (340) of prokaryotes that could serve as an information resource for research and technology applications in glycobiology. PMID:22039152

  14. 48 CFR 719.273-5 - Selection of Protégé firms.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... DEVELOPMENT SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS The U.S. Agency for International Development...-disabled veteran-owned small business, and HUBZone firms whose core competencies support USAID's mission... the quality of developmental assistance provided to Protégés, USAID reserves the right to limit...

  15. neXtProt: organizing protein knowledge in the context of human proteome projects.

    PubMed

    Gaudet, Pascale; Argoud-Puy, Ghislaine; Cusin, Isabelle; Duek, Paula; Evalet, Olivier; Gateau, Alain; Gleizes, Anne; Pereira, Mario; Zahn-Zabal, Monique; Zwahlen, Catherine; Bairoch, Amos; Lane, Lydie

    2013-01-01

    About 5000 (25%) of the ~20400 human protein-coding genes currently lack any experimental evidence at the protein level. For many others, there is only little information relative to their abundance, distribution, subcellular localization, interactions, or cellular functions. The aim of the HUPO Human Proteome Project (HPP, www.thehpp.org ) is to collect this information for every human protein. HPP is based on three major pillars: mass spectrometry (MS), antibody/affinity capture reagents (Ab), and bioinformatics-driven knowledge base (KB). To meet this objective, the Chromosome-Centric Human Proteome Project (C-HPP) proposes to build this catalog chromosome-by-chromosome ( www.c-hpp.org ) by focusing primarily on proteins that currently lack MS evidence or Ab detection. These are termed "missing proteins" by the HPP consortium. The lack of observation of a protein can be due to various factors including incorrect and incomplete gene annotation, low or restricted expression, or instability. neXtProt ( www.nextprot.org ) is a new web-based knowledge platform specific for human proteins that aims to complement UniProtKB/Swiss-Prot ( www.uniprot.org ) with detailed information obtained from carefully selected high-throughput experiments on genomic variation, post-translational modifications, as well as protein expression in tissues and cells. This article describes how neXtProt contributes to prioritize C-HPP efforts and integrates C-HPP results with other research efforts to create a complete human proteome catalog. PMID:23205526

  16. Annotation of post-translational modifications in the Swiss-Prot knowledge base.

    PubMed

    Farriol-Mathis, Nathalie; Garavelli, John S; Boeckmann, Brigitte; Duvaud, Séverine; Gasteiger, Elisabeth; Gateau, Alain; Veuthey, Anne-Lise; Bairoch, Amos

    2004-06-01

    High-throughput proteomic studies produce a wealth of new information regarding post-translational modifications (PTMs). The Swiss-Prot knowledge base is faced with the challenge of including this information in a consistent and structured way, in order to facilitate easy retrieval and promote understanding by biologist expert users as well as computer programs. We are therefore standardizing the annotation of PTM features represented in Swiss-Prot. Indeed, a controlled vocabulary has been associated with every described PTM. In this paper, we present the major update of the feature annotation, and, by showing a few examples, explain how the annotation is implemented and what it means. Mod-Prot, a future companion database of Swiss-Prot, devoted to the biological aspects of PTMs (i.e., general description of the process, identity of the modification enzyme(s), taxonomic range, mass modification) is briefly described. Finally we encourage once again the scientific community (i.e., both individual researchers and database maintainers) to interact with us, so that we can continuously enhance the quality and swiftness of our services. PMID:15174124

  17. 48 CFR 1019.202-70 - The Treasury Mentor Protégé Program.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... performance of the contract. Proposed mentor-protégé efforts will be considered during the evaluation of such... receipt by OSDBU. When submission of additional data is required during a proposal evaluation for a new contract award, shorter timeframes for submission, review and re-evaluation for approval may be...

  18. gDNA-Prot: Predict DNA-binding proteins by employing support vector machine and a novel numerical characterization of protein sequence.

    PubMed

    Zhang, Yan-Ping; Wuyunqiqige; Zheng, Wei; Liu, Shuyi; Zhao, Chunguang

    2016-10-01

    DNA-binding proteins are the functional proteins in cells, which play an important role in various essential biological activities. An effective and fast computational method gDNA-Prot is proposed to predict DNA-binding proteins in this paper, which is a DNA-binding predictor that combines the support vector machine classifier and a novel kind of feature called graphical representation. The DNA-binding protein sequence information was described with the 20 probabilities of amino acids and the 23 new numerical graphical representation features of a protein sequence, based on 23 physicochemical properties of 20 amino acids. The Principal Components Analysis (PCA) was employed as feature selection method for removing the irrelevant features and reducing redundant features. The Sigmod function and Min-max normalization methods for PCA were applied to accelerate the training speed and obtain higher accuracy. Experiments demonstrated that the Principal Components Analysis with Sigmod function generated the best performance. The gDNA-Prot method was also compared with the DNAbinder, iDNA-Prot and DNA-Prot. The results suggested that gDNA-Prot outperformed the DNAbinder and iDNA-Prot. Although the DNA-Prot outperformed gDNA-Prot, gDNA-Prot was faster and convenient to predict the DNA-binding proteins. Additionally, the proposed gNDA-Prot method is available at http://sourceforge.net/projects/gdnaprot. PMID:27378005

  19. Dosimetric properties and stability of thermoluminescent foils made from LiF:Mg,Cu,P or CaSO4:Dy during long-term use

    NASA Astrophysics Data System (ADS)

    Kłosowski, M.; Liszka, M.; Kopeć, R.; Bilski, P.; Kędzierska, D.

    2014-11-01

    A few dosimetric systems based on thermoluminescence [TL] foils were developed in recent years (Nariyama et al. 2006, Radiat. Prot. Dosim. 120, 213-218; Olko et al. 2006 Radiat. Prot. Dosim. 118, 213-218) (Czopyk et al. 2008, Radiat. Meas., 43, 977-980; Kłosowski et al. 2010, Radiat. Meas., 45, 719-721; Kopeć et al. 2013, Radiat.Meas., 56, 380-383). Major application of these systems is mapping of 2D dose distribution for medical treatment plan verification, similarly to photochromic or radiochromic films. The advantage of TL foils compared to other films is their re-usability. In this work we present dosimetric properties as dose linearity and fadding of the foils made from LiF:Mg,Cu,P or CaSO4:Dy phosphors and high temperature polymers. Both types of the foils have good linearity in the range 1-20 Gy for LiF:Mg,Cu,P and 0.1-2 Gy for CaSO4:Dy. Their long term fading does not exceed 3.7% and 9% respectively. We additionally investigated effects of sensitivity loss and emission spectra for both types of the foils. One shortcoming of TL foils is that every heat process may have negative influence on their properties, causing changes of their sensitivity. Register signal of the foils after 15 readouts may be reduced by 16% of the initial. We consider that the main reason of these changes is oxidation of organic contamination on the surface and degradation of a polymer which is one of the components of the foils. Effect of sensitivity decreasing may be slowed down by proper use and cleaning detectors by solvent.

  20. Infrastructure for the life sciences: design and implementation of the UniProt website

    PubMed Central

    Jain, Eric; Bairoch, Amos; Duvaud, Severine; Phan, Isabelle; Redaschi, Nicole; Suzek, Baris E; Martin, Maria J; McGarvey, Peter; Gasteiger, Elisabeth

    2009-01-01

    Background The UniProt consortium was formed in 2002 by groups from the Swiss Institute of Bioinformatics (SIB), the European Bioinformatics Institute (EBI) and the Protein Information Resource (PIR) at Georgetown University, and soon afterwards the website was set up as a central entry point to UniProt resources. Requests to this address were redirected to one of the three organisations' websites. While these sites shared a set of static pages with general information about UniProt, their pages for searching and viewing data were different. To provide users with a consistent view and to cut the cost of maintaining three separate sites, the consortium decided to develop a common website for UniProt. Following several years of intense development and a year of public beta testing, the domain was switched to the newly developed site described in this paper in July 2008. Description The UniProt consortium is the main provider of protein sequence and annotation data for much of the life sciences community. The website is the primary access point to this data and to documentation and basic tools for the data. These tools include full text and field-based text search, similarity search, multiple sequence alignment, batch retrieval and database identifier mapping. This paper discusses the design and implementation of the new website, which was released in July 2008, and shows how it improves data access for users with different levels of experience, as well as to machines for programmatic access. is open for both academic and commercial use. The site was built with open source tools and libraries. Feedback is very welcome and should be sent to help@uniprot.org. Conclusion The new UniProt website makes accessing and understanding UniProt easier than ever. The two main lessons learned are that getting the basics right for such a data provider website has huge benefits, but is not trivial and easy to underestimate, and that there is no substitute for using empirical data

  1. Prot-Prop: J-tool to predict the subcellular location of proteins based on physiochemical characterization.

    PubMed

    Senthilkumar, Brindha; Sailo, Sangzuala; Guruswami, Gurusubramanian; Nachimuthu, Senthilkumar

    2012-12-01

    PROT-PROP is a computational tool to characterize 27 physicochemical properties of a protein along with its subcellular location (intra or extra) in a single-window application. Other significant features of this software include calculation of numerical values for hydrophobicity, hydrophilicity; composition of small and large amino acids; net hydrophobic content in terms of low/high; and Navie's algorithm to calculate theoretical pI. PROT-PROP is an easy-to-install platform independent implementation of JAVA under a user-friendly interface. It is a standalone version as a virtual appliance and source code for platforms supporting Java 1.5.0 and higher versions, and downloadable from the web http://www.mzu.edu.in/schools/biotechnology.html . PROT-PROP can run under Windows and Macintosh Operating Systems. PROT-PROP is distributed with its source code so that it may be adapted or customized, if desired. PMID:23354819

  2. ProtAnnot: an App for Integrated Genome Browser to display how alternative splicing and transcription affect proteins

    PubMed Central

    Mall, Tarun; Eckstein, John; Norris, David; Vora, Hiral; Freese, Nowlan H.; Loraine, Ann E.

    2016-01-01

    Summary: One gene can produce multiple transcript variants encoding proteins with different functions. To facilitate visual analysis of transcript variants, we developed ProtAnnot, which shows protein annotations in the context of genomic sequence. ProtAnnot searches InterPro and displays profile matches (protein annotations) alongside gene models, exposing how alternative promoters, splicing and 3′ end processing add, remove, or remodel functional motifs. To draw attention to these effects, ProtAnnot color-codes exons by frame and displays a cityscape graphic summarizing exonic sequence at each position. These techniques make visual analysis of alternative transcripts faster and more convenient for biologists. Availability and implementation: ProtAnnot is a plug-in App for Integrated Genome Browser, an open source desktop genome browser available from http://www.bioviz.org. Contact: aloraine@uncc.edu PMID:27153567

  3. 49 CFR 26.35 - What role do business development and mentor-protégé programs have in the DBE program?

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 1 2013-10-01 2013-10-01 false What role do business development and mentor-protÃ... What role do business development and mentor-protégé programs have in the DBE program? (a) You may or... BDP or separately, you may establish a “mentor-protégé” program, in which another DBE or non-DBE...

  4. 49 CFR 26.35 - What role do business development and mentor-protégé programs have in the DBE program?

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 1 2011-10-01 2011-10-01 false What role do business development and mentor-protÃ... What role do business development and mentor-protégé programs have in the DBE program? (a) You may or... BDP or separately, you may establish a “mentor-protégé” program, in which another DBE or non-DBE...

  5. 49 CFR 26.35 - What role do business development and mentor-protégé programs have in the DBE program?

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 1 2010-10-01 2010-10-01 false What role do business development and mentor-protÃ... What role do business development and mentor-protégé programs have in the DBE program? (a) You may or... BDP or separately, you may establish a “mentor-protégé” program, in which another DBE or non-DBE...

  6. 49 CFR 26.35 - What role do business development and mentor-protégé programs have in the DBE program?

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 1 2012-10-01 2012-10-01 false What role do business development and mentor-protÃ... What role do business development and mentor-protégé programs have in the DBE program? (a) You may or... BDP or separately, you may establish a “mentor-protégé” program, in which another DBE or non-DBE...

  7. 49 CFR 26.35 - What role do business development and mentor-protégé programs have in the DBE program?

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 1 2014-10-01 2014-10-01 false What role do business development and mentor-protÃ... What role do business development and mentor-protégé programs have in the DBE program? (a) You may or... BDP or separately, you may establish a “mentor-protégé” program, in which another DBE or non-DBE...

  8. Slow pyrolysis of prot, alkali and dealkaline lignins for production of chemicals.

    PubMed

    Biswas, Bijoy; Singh, Rawel; Kumar, Jitendra; Khan, Adnan Ali; Krishna, Bhavya B; Bhaskar, Thallada

    2016-08-01

    Effect of different lignins were studied during slow pyrolysis. Maximum bio-oil yield of 31.2, 34.1, and 29.5wt.% was obtained at 350, 450 and 350°C for prot lignin, alkali lignin and dealkaline lignin respectively. Maximum yield of phenolic compounds 78%, 80% and 92% from prot lignin, alkali and dealkaline lignin at 350, 450 and 350°C. The differences in the pyrolysis products indicated the source of lignins such as soft and hard wood lignins. The biochar characterisation revealed that the various ether linkages were broken during pyrolysis and lignin was converted into monomeric substituted phenols. Bio-oil showed that the relative contents of each phenolic compound changes significantly with pyrolysis temperature and also the relative contents of each compound changes with different samples. PMID:26873286

  9. High-quality protein knowledge resource: SWISS-PROT and TrEMBL.

    PubMed

    O'Donovan, Claire; Martin, Maria Jesus; Gattiker, Alexandre; Gasteiger, Elisabeth; Bairoch, Amos; Apweiler, Rolf

    2002-09-01

    SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc.), a minimal level of redundancy and a high level of integration with other databases. Together with its automatically annotated supplement TrEMBL, it provides a comprehensive and high-quality view of the current state of knowledge about proteins. Ongoing developments include the further improvement of functional and automatic annotation in the databases including evidence attribution with particular emphasis on the human, archaeal and bacterial proteomes and the provision of additional resources such as the International Protein Index (IPI) and XML format of SWISS-PROT and TrEMBL to the user community. PMID:12230036

  10. Protein variety and functional diversity: Swiss-Prot annotation in its biological context.

    PubMed

    Boeckmann, Brigitte; Blatter, Marie-Claude; Famiglietti, Livia; Hinz, Ursula; Lane, Lydie; Roechert, Bernd; Bairoch, Amos

    2005-01-01

    We all know that the dogma 'one gene, one protein' is obsolete. A functional protein and, likewise, a protein's ultimate function depend not only on the underlying genetic information but also on the ongoing conditions of the cellular system. Frequently the transcript, like the polypeptide, is processed in multiple ways, but only one or a few out of a multitude of possible variants are produced at a time. An overview on processes that can lead to sequence variety and structural diversity in eukaryotes is given. The UniProtKB/Swiss-Prot protein knowledgebase provides a wealth of information regarding protein variety, function and associated disorders. Examples for such annotation are shown and further ones are available at http://www.expasy.org/sprot/tutorial/examples_CRB. PMID:16286078

  11. Data-poor categorization and passage retrieval for Gene Ontology Annotation in Swiss-Prot

    PubMed Central

    Ehrler, Frédéric; Geissbühler, Antoine; Jimeno, Antonio; Ruch, Patrick

    2005-01-01

    Background In the context of the BioCreative competition, where training data were very sparse, we investigated two complementary tasks: 1) given a Swiss-Prot triplet, containing a protein, a GO (Gene Ontology) term and a relevant article, extraction of a short passage that justifies the GO category assignement; 2) given a Swiss-Prot pair, containing a protein and a relevant article, automatic assignement of a set of categories. Methods Sentence is the basic retrieval unit. Our classifier computes a distance between each sentence and the GO category provided with the Swiss-Prot entry. The Text Categorizer computes a distance between each GO term and the text of the article. Evaluations are reported both based on annotator judgements as established by the competition and based on mean average precision measures computed using a curated sample of Swiss-Prot. Results Our system achieved the best recall and precision combination both for passage retrieval and text categorization as evaluated by official evaluators. However, text categorization results were far below those in other data-poor text categorization experiments The top proposed term is relevant in less that 20% of cases, while categorization with other biomedical controlled vocabulary, such as the Medical Subject Headings, we achieved more than 90% precision. We also observe that the scoring methods used in our experiments, based on the retrieval status value of our engines, exhibits effective confidence estimation capabilities. Conclusion From a comparative perspective, the combination of retrieval and natural language processing methods we designed, achieved very competitive performances. Largely data-independent, our systems were no less effective that data-intensive approaches. These results suggests that the overall strategy could benefit a large class of information extraction tasks, especially when training data are missing. However, from a user perspective, results were disappointing. Further

  12. Protótipo do primeiro interferômetro brasileiro - BDA

    NASA Astrophysics Data System (ADS)

    Cecatto, J. R.; Fernandes, F. C. R.; Neri, J. A. C. F.; Bethi, N.; Felipini, N. S.; Madsen, F. R. H.; Andrade, M. C.; Soares, A. C.; Alonso, E. M. B., Sawant, H. S.

    2004-04-01

    A interferometria é uma poderosa ferramenta usada para investigar estruturas espaciais de fontes astrofísicas fornecendo uma riqueza de detalhes inatingível pelas técnicas convencionais de imageamento. Em particular, a interferometria com ondas de rádio abre o horizonte de conhecimento do Universo nesta ampla banda do espectro eletromagnético, que vai de cerca de 20 kHz até centenas de GHz já próximo ao infravermelho, e que está acessível a partir de instrumentos instalados em solo. Neste trabalho, apresentamos o interferômetro designado por Arranjo Decimétrico Brasileiro (BDA). Trata-se do primeiro interferômetro a ser desenvolvido no Brasil e América Latina que já está em operação na fase de protótipo. Apresentamos o desenvolvimento realizado até o momento, o sítio de instalação do instrumento, o protótipo e os principais resultados dos testes de sua operação, as perspectivas futuras e a ciência a ser desenvolvida com o instrumento nas fases II e III. Neste trabalho é dada ênfase ao desenvolvimento, testes de operação e principais resultados do protótipo. É discutida brevemente a ciência que pode ser feita com o instrumento. Tanto os detalhes técnicos quanto os principais parâmetros estimados para o instrumento nas próximas fases de desenvolvimento e o desempenho do protótipo serão publicados em breve.

  13. WebProtégé: A Collaborative Ontology Editor and Knowledge Acquisition Tool for the Web

    PubMed Central

    Tudorache, Tania; Nyulas, Csongor; Noy, Natalya F.; Musen, Mark A.

    2012-01-01

    In this paper, we present WebProtégé—a lightweight ontology editor and knowledge acquisition tool for the Web. With the wide adoption of Web 2.0 platforms and the gradual adoption of ontologies and Semantic Web technologies in the real world, we need ontology-development tools that are better suited for the novel ways of interacting, constructing and consuming knowledge. Users today take Web-based content creation and online collaboration for granted. WebProtégé integrates these features as part of the ontology development process itself. We tried to lower the entry barrier to ontology development by providing a tool that is accessible from any Web browser, has extensive support for collaboration, and a highly customizable and pluggable user interface that can be adapted to any level of user expertise. The declarative user interface enabled us to create custom knowledge-acquisition forms tailored for domain experts. We built WebProtégé using the existing Protégé infrastructure, which supports collaboration on the back end side, and the Google Web Toolkit for the front end. The generic and extensible infrastructure allowed us to easily deploy WebProtégé in production settings for several projects. We present the main features of WebProtégé and its architecture and describe briefly some of its uses for real-world projects. WebProtégé is free and open source. An online demo is available at http://webprotege.stanford.edu. PMID:23807872

  14. ChemProt-3.0: a global chemical biology diseases mapping.

    PubMed

    Kringelum, Jens; Kjaerulff, Sonny Kim; Brunak, Søren; Lund, Ole; Oprea, Tudor I; Taboureau, Olivier

    2016-01-01

    ChemProt is a publicly available compilation of chemical-protein-disease annotation resources that enables the study of systems pharmacology for a small molecule across multiple layers of complexity from molecular to clinical levels. In this third version, ChemProt has been updated to more than 1.7 million compounds with 7.8 million bioactivity measurements for 19,504 proteins. Here, we report the implementation of global pharmacological heatmap, supporting a user-friendly navigation of chemogenomics space. This facilitates the visualization and selection of chemicals that share similar structural properties. In addition, the user has the possibility to search by compound, target, pathway, disease and clinical effect. Genetic variations associated to target proteins were integrated, making it possible to plan pharmacogenetic studies and to suggest human response variability to drug. Finally, Quantitative Structure-Activity Relationship models for 850 proteins having sufficient data were implemented, enabling secondary pharmacological profiling predictions from molecular structure. Database URL: http://potentia.cbs.dtu.dk/ChemProt/. PMID:26876982

  15. ProtPOS: a python package for the prediction of protein preferred orientation on a surface

    PubMed Central

    Ngai, Jimmy C. F.; Mak, Pui-In; Siu, Shirley W. I.

    2016-01-01

    Summary: Atomistic molecular dynamics simulation is a promising technique to investigate the energetics and dynamics in the protein–surface adsorption process which is of high relevance to modern biotechnological applications. To increase the chance of success in simulating the adsorption process, favorable orientations of the protein at the surface must be determined. Here, we present ProtPOS which is a lightweight and easy-to-use python package that can predict low-energy protein orientations on a surface of interest. It combines a fast conformational sampling algorithm with the energy calculation of GROMACS. The advantage of ProtPOS is it allows users to select any force fields suitable for the system at hand and provide structural output readily available for further simulation studies. Availability and Implementation: ProtPOS is freely available for academic and non-profit uses at http://cbbio.cis.umac.mo/software/protpos Supplementary information: Supplementary data are available at Bioinformatics online. Contact: shirleysiu@umac.mo PMID:27153619

  16. ChemProt-3.0: a global chemical biology diseases mapping

    PubMed Central

    Kringelum, Jens; Kjaerulff, Sonny Kim; Brunak, Søren; Lund, Ole; Oprea, Tudor I.; Taboureau, Olivier

    2016-01-01

    ChemProt is a publicly available compilation of chemical-protein-disease annotation resources that enables the study of systems pharmacology for a small molecule across multiple layers of complexity from molecular to clinical levels. In this third version, ChemProt has been updated to more than 1.7 million compounds with 7.8 million bioactivity measurements for 19 504 proteins. Here, we report the implementation of global pharmacological heatmap, supporting a user-friendly navigation of chemogenomics space. This facilitates the visualization and selection of chemicals that share similar structural properties. In addition, the user has the possibility to search by compound, target, pathway, disease and clinical effect. Genetic variations associated to target proteins were integrated, making it possible to plan pharmacogenetic studies and to suggest human response variability to drug. Finally, Quantitative Structure–Activity Relationship models for 850 proteins having sufficient data were implemented, enabling secondary pharmacological profiling predictions from molecular structure. Database URL: http://potentia.cbs.dtu.dk/ChemProt/ PMID:26876982

  17. FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants.

    PubMed

    Bednar, David; Beerens, Koen; Sebestova, Eva; Bendl, Jaroslav; Khare, Sagar; Chaloupkova, Radka; Prokop, Zbynek; Brezovsky, Jan; Baker, David; Damborsky, Jiri

    2015-11-01

    There is great interest in increasing proteins' stability to enhance their utility as biocatalysts, therapeutics, diagnostics and nanomaterials. Directed evolution is a powerful, but experimentally strenuous approach. Computational methods offer attractive alternatives. However, due to the limited reliability of predictions and potentially antagonistic effects of substitutions, only single-point mutations are usually predicted in silico, experimentally verified and then recombined in multiple-point mutants. Thus, substantial screening is still required. Here we present FireProt, a robust computational strategy for predicting highly stable multiple-point mutants that combines energy- and evolution-based approaches with smart filtering to identify additive stabilizing mutations. FireProt's reliability and applicability was demonstrated by validating its predictions against 656 mutations from the ProTherm database. We demonstrate that thermostability of the model enzymes haloalkane dehalogenase DhaA and γ-hexachlorocyclohexane dehydrochlorinase LinA can be substantially increased (ΔTm = 24°C and 21°C) by constructing and characterizing only a handful of multiple-point mutants. FireProt can be applied to any protein for which a tertiary structure and homologous sequences are available, and will facilitate the rapid development of robust proteins for biomedical and biotechnological applications. PMID:26529612

  18. PROGRESSION OF REGULATORY GENE EXPRESSION STATES IN FETAL AND ADULT PRO-T CELL DEVELOPMENT

    PubMed Central

    David-Fung, Elizabeth-Sharon; Yui, Mary A.; Morales, Marissa; Wang, Hua; Taghon, Tom; Diamond, Rochelle A.; Rothenberg, Ellen V.

    2014-01-01

    Precursors entering the T-cell developmental pathway traverse a progression of states characterized by distinctive patterns of gene expression. Of particular interest are regulatory genes, which ultimately control the dwell time of cells in each state and establish the mechanisms that propel them forward to subsequent states. Under particular genetic and developmental circumstances, the transitions between these states occur with different timing, and environmental feedbacks may shift the steady-state accumulations of cells in each state. The fetal transit through pro-T cell stages is faster than in the adult, and subject to somewhat different genetic requirements. To explore causes of such variation, this review presents previously unpublished data on differentiation gene activation in pro-T cells of pre-TCR deficient mutant mice, and a quantitative comparison of the profiles of transcription factor gene expression in pro-T cell subsets of fetal and adult wildtype mice. Against a background of consistent gene expression, several regulatory genes show marked differences between fetal and adult expression profiles, including those encoding two bHLH antagonist Id factors, the Ets family factor SpiB, and the Notch target gene Deltex1. The results also reveal global differences in regulatory alterations triggered by the first TCR-dependent selection events in fetal and adult thymopoiesis. PMID:16448545

  19. LiF:Mg,Ti TLD response as a function of photon energy for moderately filtered x-ray spectra in the range of 20-250 kVp relative to {sup 60}Co

    SciTech Connect

    Nunn, A. A.; Davis, S. D.; Micka, J. A.; DeWerd, L. A.

    2008-05-15

    The response of LiF:Mg,Ti thermoluminescent dosimeters (TLDs) as a function of photon energy was determined using irradiations with moderately filtered x-ray beams in the energy range of 20-250 kVp relative to the response to irradiations with {sup 60}Co photons. To determine if the relative light output from LiF:Mg,Ti TLDs per unit air kerma as a function of photon energy can be predicted using calculations such as Monte Carlo (MC) simulations, measurements from the x-ray beam irradiations were compared with MC calculated results, similar to the methodology used by Davis et al. [Radiat. Prot. Dosim. 106, 33-43 (2003)]. TLDs were irradiated in photon beams with well-known air kerma rates using the National Institute of Standards and Technology traceable M-series x-ray beams in the range of 20-250 kVp. For each x-ray beam, several sets of TLDs were irradiated for times corresponding to different air kerma levels to take into account any dose nonlinearity. TLD light output was then compared to that from several sets of TLDs irradiated at similar corresponding air kerma levels using a {sup 60}Co irradiator. The MC code MCNP5 was used to account for photon scatter and attenuation in the holder and TLDs and was used to calculate the predicted relative TLD light output per unit air kerma for irradiations with each of the experimentally used photon beams. The measured relative TLD response as a function of photon energy differed by up to 13% from the MC calculations. We conclude that MC calculations do not accurately predict the relative response of TLDs as a function of photon energy, consistent with the conclusions of Davis et al. [Radiat. Prot. Dosim. 106, 33-43 (2003)]. This is likely due to complications in the solid state physics of the thermoluminescence process that are not incorporated into the simulation.

  20. 76 FR 25733 - 30-Day Notice of Proposed Information Collection DS 4053, Department of State Mentor-Protégé...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-05

    ... Notice of Proposed Information Collection DS 4053, Department of State Mentor-Prot g Program Application.... Title of Information Collection: Department of State Mentor-Prot g Program Application. OMB Control...-4053. Respondents: Small and large for-profit companies planning to team together in an official...

  1. 48 CFR 653.219-71 - DOS form DS-4053, Department of State Mentor-Protégé Program Application.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ..., Department of State Mentor-Protégé Program Application. 653.219-71 Section 653.219-71 Federal Acquisition...-4053, Department of State Mentor-Protégé Program Application. As prescribed in 619.102-70(i), DS-4053 is prescribed for use in applying for an agreement under the Department of State...

  2. 48 CFR 653.219-71 - DOS form DS-4053, Department of State Mentor-Protégé Program Application.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ..., Department of State Mentor-Protégé Program Application. 653.219-71 Section 653.219-71 Federal Acquisition...-4053, Department of State Mentor-Protégé Program Application. As prescribed in 619.102-70(i), DS-4053 is prescribed for use in applying for an agreement under the Department of State...

  3. 48 CFR 3052.219-72 - Evaluation of prime contractor participation in the DHS mentor-protégé program.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... Evaluation of prime contractor participation in the DHS mentor-protégé program. As prescribed in (HSAR) 48 CFR 3019.708-70(c), insert the following provision: Evaluation of Prime Contractor Participation in... contractor participation in the DHS mentor-protégé program. 3052.219-72 Section 3052.219-72...

  4. 48 CFR 3052.219-72 - Evaluation of prime contractor participation in the DHS mentor-protégé program.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... Evaluation of prime contractor participation in the DHS mentor-protégé program. As prescribed in (HSAR) 48 CFR 3019.708-70(c), insert the following provision: Evaluation of Prime Contractor Participation in... contractor participation in the DHS mentor-protégé program. 3052.219-72 Section 3052.219-72...

  5. 48 CFR 3052.219-72 - Evaluation of prime contractor participation in the DHS mentor-protégé program.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... Evaluation of prime contractor participation in the DHS mentor-protégé program. As prescribed in (HSAR) 48 CFR 3019.708-70(c), insert the following provision: Evaluation of Prime Contractor Participation in... contractor participation in the DHS mentor-protégé program. 3052.219-72 Section 3052.219-72...

  6. 48 CFR 653.219-71 - DOS form DS-4053, Department of State Mentor-Protégé Program Application.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ..., Department of State Mentor-Protégé Program Application. 653.219-71 Section 653.219-71 Federal Acquisition...-4053, Department of State Mentor-Protégé Program Application. As prescribed in 619.102-70(i), DS-4053 is prescribed for use in applying for an agreement under the Department of State...

  7. 48 CFR 3052.219-72 - Evaluation of prime contractor participation in the DHS mentor-protégé program.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... Evaluation of prime contractor participation in the DHS mentor-protégé program. As prescribed in (HSAR) 48 CFR 3019.708-70(c), insert the following provision: Evaluation of Prime Contractor Participation in... contractor participation in the DHS mentor-protégé program. 3052.219-72 Section 3052.219-72...

  8. 48 CFR 3052.219-72 - Evaluation of prime contractor participation in the DHS mentor-protégé program.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Evaluation of prime contractor participation in the DHS mentor-protégé program. As prescribed in (HSAR) 48 CFR 3019.708-70(c), insert the following provision: Evaluation of Prime Contractor Participation in... contractor participation in the DHS mentor-protégé program. 3052.219-72 Section 3052.219-72...

  9. 48 CFR 653.219-71 - DOS form DS-4053, Department of State Mentor-Protégé Program Application.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ..., Department of State Mentor-Protégé Program Application. 653.219-71 Section 653.219-71 Federal Acquisition...-4053, Department of State Mentor-Protégé Program Application. As prescribed in 619.102-70(i), DS-4053 is prescribed for use in applying for an agreement under the Department of State...

  10. 48 CFR 653.219-71 - DOS form DS-4053, Department of State Mentor-Protégé Program Application.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ..., Department of State Mentor-Protégé Program Application. 653.219-71 Section 653.219-71 Federal Acquisition...-4053, Department of State Mentor-Protégé Program Application. As prescribed in 619.102-70(i), DS-4053 is prescribed for use in applying for an agreement under the Department of State...

  11. What Do Hispanic Students Want in a Mentor? A Model of Protégé Cultural Orientation, Mentorship Expectations, and Performance

    ERIC Educational Resources Information Center

    Cox, Cody B.; Yang, Yan; Dicke-Bohmann, Amy K.

    2014-01-01

    The purpose of this study was to propose and test a model of the effects of cultural factors on Hispanic protégés' expectations for and experiences with their mentors. Specifically, the proposed model posits that cultural orientation predicts the mentorship functions protégés desire, and the positive impact of these mentorship functions…

  12. Protégés' Personality Traits, Expectations, the Quality of the Mentoring Relationship and Adjustment: A Big Five Analysis

    ERIC Educational Resources Information Center

    Goldner, Limor

    2016-01-01

    Background: Community-based mentoring interventions can benefit high-risk youth. However, meta-analyses suggest that these benefits may be conditioned by protégés' personality. Objectives: Associations between protégés' personality traits and mentoring expectations, the quality of the mentoring relationship, the perceived mentoring contribution,…

  13. ProtPhylo: identification of protein–phenotype and protein–protein functional associations via phylogenetic profiling

    PubMed Central

    Cheng, Yiming; Perocchi, Fabiana

    2015-01-01

    ProtPhylo is a web-based tool to identify proteins that are functionally linked to either a phenotype or a protein of interest based on co-evolution. ProtPhylo infers functional associations by comparing protein phylogenetic profiles (co-occurrence patterns of orthology relationships) for more than 9.7 million non-redundant protein sequences from all three domains of life. Users can query any of 2048 fully sequenced organisms, including 1678 bacteria, 255 eukaryotes and 115 archaea. In addition, they can tailor ProtPhylo to a particular kind of biological question by choosing among four main orthology inference methods based either on pair-wise sequence comparisons (One-way Best Hits and Best Reciprocal Hits) or clustering of orthologous proteins across multiple species (OrthoMCL and eggNOG). Next, ProtPhylo ranks phylogenetic neighbors of query proteins or phenotypic properties using the Hamming distance as a measure of similarity between pairs of phylogenetic profiles. Candidate hits can be easily and flexibly prioritized by complementary clues on subcellular localization, known protein–protein interactions, membrane spanning regions and protein domains. The resulting protein list can be quickly exported into a csv text file for further analyses. ProtPhylo is freely available at http://www.protphylo.org. PMID:25956654

  14. The annotation of both human and mouse kinomes in UniProtKB/Swiss-Prot: one small step in manual annotation, one giant leap for full comprehension of genomes.

    PubMed

    Braconi Quintaje, Silvia; Orchard, Sandra

    2008-08-01

    Biomolecule phosphorylation by protein kinases is a fundamental cell signaling process in all living cells. Following the comprehensive cataloguing of the protein kinase complement of the human genome (Manning, G., Whyte, D. B., Martinez, R., Hunter, T., and Sudarsanam, S. (2002) The protein kinase complement of the human genome. Science 298, 1912-1934), this review will detail the state-of-the-art human and mouse kinase proteomes as provided in the UniProtKB/Swiss-Prot protein knowledgebase. The sequences of the 480 classical and up to 24 atypical protein kinases now believed to exist in the human genome and 484 classical and up to 24 atypical kinases within the mouse genome have been reviewed and, where necessary, revised. Extensive annotation has been added to each entry. In an era when a wealth of new databases is emerging on the Internet, UniProtKB/Swiss-Prot makes available to the scientific community the most up-to-date and in-depth annotation of these proteins with access to additional external resources linked from within each entry. Incorrect sequence annotations resulting from errors and artifacts have been eliminated. Each entry will be constantly reviewed and updated as new information becomes available with the orthologous enzymes in related species being annotated in a parallel effort and complete kinomes being completed as sequences become available. This ensures that the mammalian kinomes available from UniProtKB/Swiss-Prot are of a consistently high standard with each separate entry acting both as a valuable information resource and a central portal to a wealth of further detail via extensive cross-referencing. PMID:18436524

  15. The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants.

    PubMed

    Yip, Yum L; Scheib, Holger; Diemand, Alexander V; Gattiker, Alexandre; Famiglietti, Livia M; Gasteiger, Elisabeth; Bairoch, Amos

    2004-05-01

    Missense mutation leading to single amino acid polymorphism (SAP) is the type of mutation most frequently related to human diseases. The Swiss-Prot protein knowledgebase records information on such mutations in various sections of a protein entry, namely in the "feature," "comment," and "reference" fields. To facilitate users in obtaining the most relevant information about each human SAP recorded in the knowledgebase, the Swiss-Prot Variant web pages were created to provide a summary of available sequence information, as well as additional structural information on each variant. In particular, the ModSNP database was set up to store information related to SAPs and to manage the modeling of SAPs onto protein structures via an automatic homology modeling pipeline. Currently, among the 16,566 human SAPs recorded in the Swiss-Prot knowledgebase (release 42.5, 21 November 2003), more than 25% have corresponding 3D-models. Of these variants, 47% are related to disease, 26% are polymorphisms, and 27% are not yet clearly classified. The ModSNP database is updated and the subsequent model construction pipeline is launched with each weekly Swiss-Prot release. Thus, the ModSNP database represents a valuable resource for the structural analysis of protein variation. The Swiss-Prot variant pages are accessible from the NiceProt view of a Swiss-Prot entry on the ExPASy server (www.expasy.org/), via a hyperlink created for the stable and unique identifier FTId of each human SAP. PMID:15108278

  16. 13 CFR 124.520 - What are the rules governing SBA's Mentor/Protégé program?

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... agreement under 2 CFR 180.800(b). Miscellaneous Reporting Requirements ... plan, and to improve its ability to successfully compete for contracts. (b) Mentors. Any concern or non... protégé firm meet the goals established in its SBA-approved business plan; (ii) Establish a single...

  17. 13 CFR 124.520 - What are the rules governing SBA's Mentor/Protégé program?

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... agreement under 2 CFR 180.800(b). ... plan, and to improve its ability to successfully compete for contracts. (b) Mentors. Any concern or non... protégé firm meet the goals established in its SBA-approved business plan; (ii) Establish a single...

  18. 13 CFR 124.520 - What are the rules governing SBA's Mentor/Protégé program?

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... agreement under 2 CFR 180.800(b). Miscellaneous Reporting Requirements ... plan, and to improve its ability to successfully compete for contracts. (b) Mentors. Any concern or non... protégé firm meet the goals established in its SBA-approved business plan; (ii) Establish a single...

  19. 78 FR 69171 - 60-Day Notice of Proposed Information Collection: Department of State Mentor Protégé Program...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-18

    ... forms of information technology. Please note that comments submitted in response to this Notice are... Notice of Proposed Information Collection: Department of State Mentor Prot g Program Application ACTION... and Budget (OMB) approval for the information collection described below. In accordance with...

  20. Domain ontologies in software engineering: use of Protégé with the EON architecture.

    PubMed

    Musen, M A

    1998-11-01

    Domain ontologies are formal descriptions of the classes of concepts and the relationships among those concepts that describe an application area. The Protégé software-engineering methodology provides a clear division between domain ontologies and domain-independent problem-solvers that, when mapped to domain ontologies, can solve application tasks. The Protégé approach allows domain ontologies to inform the total software-engineering process, and for ontologies to be shared among a variety of problem-solving components. We illustrate the approach by describing the development of EON, a set of middleware components that automate various aspects of protocol-directed therapy. Our work illustrates the organizing effect that domain ontologies can have on the software-development process. Ontologies, like all formal representations, have limitations in their ability to capture the semantics of application areas. Nevertheless, the capability of ontologies to encode clinical distinctions not usually captured by controlled medical terminologies provides significant advantages for developers and maintainers of clinical software applications. PMID:9865052

  1. SubCellProt: predicting protein subcellular localization using machine learning approaches.

    PubMed

    Garg, Prabha; Sharma, Virag; Chaudhari, Pradeep; Roy, Nilanjan

    2009-01-01

    High-throughput genome sequencing projects continue to churn out enormous amounts of raw sequence data. However, most of this raw sequence data is unannotated and, hence, not very useful. Among the various approaches to decipher the function of a protein, one is to determine its localization. Experimental approaches for proteome annotation including determination of a protein's subcellular localizations are very costly and labor intensive. Besides the available experimental methods, in silico methods present alternative approaches to accomplish this task. Here, we present two machine learning approaches for prediction of the subcellular localization of a protein from the primary sequence information. Two machine learning algorithms, k Nearest Neighbor (k-NN) and Probabilistic Neural Network (PNN) were used to classify an unknown protein into one of the 11 subcellular localizations. The final prediction is made on the basis of a consensus of the predictions made by two algorithms and a probability is assigned to it. The results indicate that the primary sequence derived features like amino acid composition, sequence order and physicochemical properties can be used to assign subcellular localization with a fair degree of accuracy. Moreover, with the enhanced accuracy of our approach and the definition of a prediction domain, this method can be used for proteome annotation in a high throughput manner. SubCellProt is available at www.databases.niper.ac.in/SubCellProt. PMID:19537160

  2. Teachable Agents and the Protégé Effect: Increasing the Effort Towards Learning

    NASA Astrophysics Data System (ADS)

    Chase, Catherine C.; Chin, Doris B.; Oppezzo, Marily A.; Schwartz, Daniel L.

    2009-08-01

    Betty's Brain is a computer-based learning environment that capitalizes on the social aspects of learning. In Betty's Brain, students instruct a character called a Teachable Agent (TA) which can reason based on how it is taught. Two studies demonstrate the protégé effect: students make greater effort to learn for their TAs than they do for themselves. The first study involved 8th-grade students learning biology. Although all students worked with the same Betty's Brain software, students in the TA condition believed they were teaching their TAs, while in another condition, they believed they were learning for themselves. TA students spent more time on learning activities (e.g., reading) and also learned more. These beneficial effects were most pronounced for lower achieving children. The second study used a verbal protocol with 5th-grade students to determine the possible causes of the protégé effect. As before, students learned either for their TAs or for themselves. Like study 1, students in the TA condition spent more time on learning activities. These children treated their TAs socially by attributing mental states and responsibility to them. They were also more likely to acknowledge errors by displaying negative affect and making attributions for the causes of failures. Perhaps having a TA invokes a sense of responsibility that motivates learning, provides an environment in which knowledge can be improved through revision, and protects students' egos from the psychological ramifications of failure.

  3. SynProt: A Database for Proteins of Detergent-Resistant Synaptic Protein Preparations

    PubMed Central

    Pielot, Rainer; Smalla, Karl-Heinz; Müller, Anke; Landgraf, Peter; Lehmann, Anne-Christin; Eisenschmidt, Elke; Haus, Utz-Uwe; Weismantel, Robert; Gundelfinger, Eckart D.; Dieterich, Daniela C.

    2012-01-01

    Chemical synapses are highly specialized cell–cell contacts for communication between neurons in the CNS characterized by complex and dynamic protein networks at both synaptic membranes. The cytomatrix at the active zone (CAZ) organizes the apparatus for the regulated release of transmitters from the presynapse. At the postsynaptic side, the postsynaptic density constitutes the machinery for detection, integration, and transduction of the transmitter signal. Both pre- and postsynaptic protein networks represent the molecular substrates for synaptic plasticity. Their function can be altered both by regulating their composition and by post-translational modification of their components. For a comprehensive understanding of synaptic networks the entire ensemble of synaptic proteins has to be considered. To support this, we established a comprehensive database for synaptic junction proteins (SynProt database) primarily based on proteomics data obtained from biochemical preparations of detergent-resistant synaptic junctions. The database currently contains 2,788 non-redundant entries of rat, mouse, and some human proteins, which mainly have been manually extracted from 12 proteomic studies and annotated for synaptic subcellular localization. Each dataset is completed with manually added information including protein classifiers as well as automatically retrieved and updated information from public databases (UniProt and PubMed). We intend that the database will be used to support modeling of synaptic protein networks and rational experimental design. PMID:22737123

  4. Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining

    PubMed Central

    Hoehndorf, Robert; Martin, Maria J.; Solovyev, Victor

    2016-01-01

    The widening gap between known proteins and their functions has encouraged the development of methods to automatically infer annotations. Automatic functional annotation of proteins is expected to meet the conflicting requirements of maximizing annotation coverage, while minimizing erroneous functional assignments. This trade-off imposes a great challenge in designing intelligent systems to tackle the problem of automatic protein annotation. In this work, we present a system that utilizes rule mining techniques to predict metabolic pathways in prokaryotes. The resulting knowledge represents predictive models that assign pathway involvement to UniProtKB entries. We carried out an evaluation study of our system performance using cross-validation technique. We found that it achieved very promising results in pathway identification with an F1-measure of 0.982 and an AUC of 0.987. Our prediction models were then successfully applied to 6.2 million UniProtKB/TrEMBL reference proteome entries of prokaryotes. As a result, 663,724 entries were covered, where 436,510 of them lacked any previous pathway annotations. PMID:27390860

  5. KnotProt: a database of proteins with knots and slipknots

    PubMed Central

    Jamroz, Michal; Niemyska, Wanda; Rawdon, Eric J.; Stasiak, Andrzej; Millett, Kenneth C.; Sułkowski, Piotr; Sulkowska, Joanna I.

    2015-01-01

    The protein topology database KnotProt, http://knotprot.cent.uw.edu.pl/, collects information about protein structures with open polypeptide chains forming knots or slipknots. The knotting complexity of the cataloged proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. The pattern visible in the matrix gives the knotting fingerprint of a given protein and permits users to determine, for example, the minimal length of the knotted regions (knot's core size) or the depth of a knot, i.e. how many amino acids can be removed from either end of the cataloged protein structure before converting it from a knot to a different type of knot. In addition, the database presents extensive information about the biological functions, families and fold types of proteins with non-trivial knotting. As an additional feature, the KnotProt database enables users to submit protein or polymer chains and generate their knotting fingerprints. PMID:25361973

  6. FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants

    PubMed Central

    Sebestova, Eva; Bendl, Jaroslav; Khare, Sagar; Chaloupkova, Radka; Prokop, Zbynek; Brezovsky, Jan; Baker, David; Damborsky, Jiri

    2015-01-01

    There is great interest in increasing proteins’ stability to enhance their utility as biocatalysts, therapeutics, diagnostics and nanomaterials. Directed evolution is a powerful, but experimentally strenuous approach. Computational methods offer attractive alternatives. However, due to the limited reliability of predictions and potentially antagonistic effects of substitutions, only single-point mutations are usually predicted in silico, experimentally verified and then recombined in multiple-point mutants. Thus, substantial screening is still required. Here we present FireProt, a robust computational strategy for predicting highly stable multiple-point mutants that combines energy- and evolution-based approaches with smart filtering to identify additive stabilizing mutations. FireProt’s reliability and applicability was demonstrated by validating its predictions against 656 mutations from the ProTherm database. We demonstrate that thermostability of the model enzymes haloalkane dehalogenase DhaA and γ-hexachlorocyclohexane dehydrochlorinase LinA can be substantially increased (ΔT m = 24°C and 21°C) by constructing and characterizing only a handful of multiple-point mutants. FireProt can be applied to any protein for which a tertiary structure and homologous sequences are available, and will facilitate the rapid development of robust proteins for biomedical and biotechnological applications. PMID:26529612

  7. Modulation de l'apoptose radioinduite par Ac-DEVD-CHO, un inhibiteur de protéases ``ice-like"

    NASA Astrophysics Data System (ADS)

    Weltin, D.; Holl, V.; Hyun, J. W.; Marchal, J.; Jung, G. M.; Dufour, P.; Bischoff, P.

    1998-04-01

    The “ICE-like" proteases, recently renamed caspases, are the human homologues of the Caenorhabditis elegans ced-3 gene product and are activated in the early steps of apoptosis. The aim of this work is to determine whether the inhibition of one of these proteases, namely caspase-3, is able to modify the cell sensitivity toward radiation-induced apoptosis. Murine spleen lymphocytes submitted to γ-radiations in presence of Ac-DVED-CHO, a caspase-3 specific inhibitor, exhibit a sharply reduced number of radiation-induced hypodiploid particules as compared to the controls and an almost total inhibition of the internucleosomal DNA fragmentation. However, both the anionic phospholipids externalisation, another specific hallmark of apoptosis, and the viability remain unchanged. Les protéases “ICE-like" ou caspases, sont les homologues humaines du produit du gène ced-3 du ver Caenorhabditis elegans et sont activées lors des étapes précoces de l'apoptose. L'objectif de ce travail vise à déterminer dans quelle mesure l'inhibition de l'une d'entre elles, la caspase-3 est susceptible de modifier la sensibilité des cellules vis-à-vis de l'apoptose radioinduite. Des lymphocytes spléniques murins irradiés en présence de Ac-DVED-CHO un inhibiteur spécifique de la caspase-3 présentent un taux de particules hypodiploïdes radioinduites bien inférieur à celui des contrôles et une diminution drastique de la fragmentation internucléosomale de l'ADN. Toutefois, ni l'externalisation des phospholipides anioniques, autre marqueur spécifique de l'apoptose, ni la viabilité ne sont affectées.

  8. Prediction of G Protein-Coupled Receptors with SVM-Prot Features and Random Forest

    PubMed Central

    Ju, Ying

    2016-01-01

    G protein-coupled receptors (GPCRs) are the largest receptor superfamily. In this paper, we try to employ physical-chemical properties, which come from SVM-Prot, to represent GPCR. Random Forest was utilized as classifier for distinguishing them from other protein sequences. MEME suite was used to detect the most significant 10 conserved motifs of human GPCRs. In the testing datasets, the average accuracy was 91.61%, and the average AUC was 0.9282. MEME discovery analysis showed that many motifs aggregated in the seven hydrophobic helices transmembrane regions adapt to the characteristic of GPCRs. All of the above indicate that our machine-learning method can successfully distinguish GPCRs from non-GPCRs. PMID:27529053

  9. Prediction of G Protein-Coupled Receptors with SVM-Prot Features and Random Forest.

    PubMed

    Liao, Zhijun; Ju, Ying; Zou, Quan

    2016-01-01

    G protein-coupled receptors (GPCRs) are the largest receptor superfamily. In this paper, we try to employ physical-chemical properties, which come from SVM-Prot, to represent GPCR. Random Forest was utilized as classifier for distinguishing them from other protein sequences. MEME suite was used to detect the most significant 10 conserved motifs of human GPCRs. In the testing datasets, the average accuracy was 91.61%, and the average AUC was 0.9282. MEME discovery analysis showed that many motifs aggregated in the seven hydrophobic helices transmembrane regions adapt to the characteristic of GPCRs. All of the above indicate that our machine-learning method can successfully distinguish GPCRs from non-GPCRs. PMID:27529053

  10. Development, implementation and evaluation of a peer review of teaching (PRoT) initiative in nursing education.

    PubMed

    Mager, Diana R; Kazer, Meredith W; Conelius, Jaclyn; Shea, Joyce; Lippman, Doris T; Torosyan, Roben; Nantz, Kathryn

    2014-01-01

    For many years, an area of research in higher education has been emerging around the development and implementation of fair and effective peer evaluation programs. Recently, a new body of knowledge has developed regarding the development and implementation of fair and effective peer evaluation programs resulting in formative and summative evaluations. The purpose of this article is to describe the development, implementation, and evaluation of a peer review of teaching (PRoT) program for nursing faculty, initiated at one small comprehensive university in the northeastern United States. Pairs of nursing faculty evaluated each other's teaching, syllabi, and course materials after collaborating in a pre-evaluation conference to discuss goals of the classroom visit. Qualitative data gathered in post project focus groups revealed that faculty found their modified PRoT process to be a mutually beneficial experience that was more useful, flexible and collegial, and less stressful than their previous evaluation process. PMID:24893326