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INTREPID
An information-theoretic approach for functional site identification that exploits the information in large diverse multiple sequence alignments (MSAs). INTREPID uses a traversal of the phylogeny in combination with a positional conservation score, based on Jensen-Shannon divergence, to rank positions in an MSA. While knowledge of protein 3D structure can significantly improve the accuracy of functional site identification, since structural information is not available for a majority of proteins, INTREPID relies solely on sequence information.
DIVERGE
A software system for phylogeny-based analyses of protein family evolution and functional divergence. It provides a suite of statistical tools for selection and prioritization of the amino acid sites that are responsible for the functional divergence of a gene family. The synergistic efforts of DIVERGE and other methods have convincingly demonstrated that the pattern of rate change at a particular amino acid site may contain insightful information about the underlying functional divergence following gene duplication. These predicted sites may be used as candidates for further experiments.
SDPpred / Specificity Determining Position prediction
A tool for prediction of residues in protein sequences that determine the proteins' functional specificity. SDPpred is designed for analysis of protein families whose members have biochemically similar but not identical interaction partners (e.g. different substrates for a family of transporters). SDPpred predicts residues that could be responsible for the proteins' choice of their correct interaction partners. The input of SDPpred is a multiple alignment of a protein family divided into a number of specificity groups, within which the interaction partner is believed to be the same.
ASMC / Active Sites Modeling and Clustering
An unsupervised method to classify sequences using structural information of protein pockets. The method predicts functional amino-acids by proposing active site SDP residues (Specificity Determining Position) and active site CP residues (Conserved Positions) profiles. ASMC combines homology modeling of family members, structural alignment of modeled active sites and a subsequent hierarchical conceptual classification of obtained alignments. Comparison of profiles obtained from computed clusters allows the identification of the residues correlated to sub-families function divergence.
SubSite
Allows the user to identify subfamily determining sites (SDS) within a protein family. SubSite takes two different approaches to identify a SDS site. At first SubSite estimates the average relative conservancy of each amino acid residues in the subgroups of the protein family through a hypothetical mutational approach. SubSite next categorizes the sequence alignment columns based on their compositional complexity. Given a protein sequence alignment and its subfamily division information, SubSite predicts the potential subfamily determining sites using the above mentioned approaches.
SPrOS / Specificity Projection On Sequence
Estimates the specificity of residues to user-defined groups. SPrOS is based on a local sequence comparison method. It can recognize the amino acid residues associated with the functional groups of protein families. The tool returns an estimate of specificity to each predefined class for every amino acid position of the test sequence. It can be use in the study of mechanisms directed the specificity of proteins belonging to diverged families divided into intersecting functional groups.
BADASP / Burst After Duplication with Ancestral Sequence Predictions
Obsolete
A software package for identifying sites that may confer subfamily-specific biological functions in protein families following functional divergence of duplicated proteins. A given protein phylogeny is grouped into subfamilies based on orthology/paralogy relationships and/or user definitions. Ancestral sequences are then predicted from the sequence alignment and the functional specificity is calculated using variants of the Burst After Duplication method, which tests for radical amino acid substitutions following gene duplications that are subsequently conserved. Statistics are output along with subfamily groupings and ancestral sequences for an easy analysis with other packages.
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