AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. We have added a collection of protein contact potentials to the AAindex as a new section. Accordingly ...
PubMed Central
AAindex database of over 500 amino acid indices collected by Kanehisa [2, 3] http://www.genome.jp/ aaindex numbers have been pointed out by Halle [45]. Prediction of B-factors from the sequence using SVM
E-print Network
The division of the aminoacyl-tRNA synthetases in two classes is compared with a division of the amino acids in two classes, obtained from the AAIndex databank by a principal component analysis. The division of the enzymes in Classes I and II follows to a great extent a division in the chemical and biological properties of their ...
NASA Astrophysics Data System (ADS)
features of the amino acids associated with certain locations, based on the AAindex database [17] of amino. The Integrating SVM calculates the probability that a protein belongs to each location in a dataset. lysosome. The first three classifiers are all SVM-based. SVMTarget is similar to TargetP [15] as it ...
Informative numerical representations of amino acid residues are essential for successful in silico modeling or establishing the structure-activity relationships of proteins. A straightforward approach is adopted here for representing more than 500 amino acid indices from the AAindex database ...
PubMed
Protein SUMO modification is an important post-translational modification and the optimization of prediction methods remains a challenge. Here, by using Support Vector Machines algorithm (SVM), a novel computational method was developed for SUMO modification site prediction based on Sequential Forward Selection (SFS) of hundreds of amino acid properties, ...
BackgroundMost machine learning techniques currently applied in the literature need a fixed dimensionality of input data. However, this requirement is frequently violated by real input data, such as DNA and protein sequences, that often differ in length due to insertions and deletions. It is also notable that performance in classification and regression is often improved by numerical encoding of ...
BackgroundHydroxylation is an important post-translational modification and closely related to various diseases. Besides the biotechnology experiments, in silico prediction methods are alternative ways to identify the potential hydroxylation sites.Methodology/Principal FindingsIn this study, we developed a novel sequence-based method for identifying the two main types of hydroxylation sites � ...
Phosphorylation is one of the most important post-translational modifications, and the identification of protein phosphorylation sites is particularly important for studying disease diagnosis. However, experimental detection of phosphorylation sites is labor intensive. It would be beneficial if computational methods are available to provide an extra reference for the phosphorylation sites. Here we ...
Crimean-Congo hemorrhagic fever (CCHF) is a severe illness with high fatality. Cases are reported in several countries in Africa, Europe, the Middle East, and Asia. Phylogenetic analyses based on the virus S (nucleocapsid), M (glycoprotein), and L (polymerase) genome segments sequences indicate distinct geographic lineages exist but their specific genetic characteristics require elucidation. In ...
The prediction of protein structures is a current issue of great significance in structural bioinformatics. More specifically, the prediction of the tertiary structure of a protein consists in determining its three-dimensional conformation based solely on its amino acid sequence. This study proposes a method in which protein fragments are assembled ...
Attachment of a myristoyl group to NH(2)-terminus of a nascent protein among protein post-translational modification (PTM) is called myristoylation. The myristate moiety of proteins plays an important role for their biological functions, such as regulation of membrane binding (HIV-1 Gag) and enzyme activity (AMPK). Several predictors based on protein sequences alone are hitherto proposed. However, ...
Attachment of a myristoyl group to NH2-terminus of a nascent protein among protein post-translational modification (PTM) is called myristoylation. The myristate moiety of proteins plays an important role for their biological functions, such as regulation of membrane binding (HIV-1 Gag) and enzyme activity (AMPK). Several predictors based on protein sequences alone are ...
BackgroundExisting methods of predicting DNA-binding proteins used valuable features of physicochemical properties to design support vector machine (SVM) based classifiers. Generally, selection of physicochemical properties and determination of their corresponding feature vectors rely mainly on known properties of binding mechanism and experience of designers. However, there exists a troublesome ...
BackgroundAmyloid fibrillar aggregates of proteins or polypeptides are known to be associated with many human diseases. Recent studies suggest that short protein regions trigger this aggregation. Thus, identifying these short peptides is critical for understanding diseases and finding potential therapeutic targets.ResultsWe propose a method, named Pafig (Prediction of amyloid fibril-forming ...
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NBII National Biological Information Infrastructure
... Abstract : The amino acid composition of botulinum toxin ... of the automatic amino acid analyzer. ... Descriptors : *AMINO ACIDS, *BACTERIAL TOXINS ...
DTIC Science & Technology
... Accession Number : AD0449728. Title : AMINO ACID COMPOSITION AND TERMINAL AMINO ACIDS OF STAPHYLOCOCCAL ENTEROTOXIN B. ...
