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Functional site detection software tools | Protein structure data analysis

The structure and function of proteins underlie most aspects of biology and their mutational perturbations often cause disease. To identify the molecular determinants of function as well as targets for drugs, it is central to characterize the…
SIMBAL
Desktop

SIMBAL

Allows for follow-up investigation in silico once correlations have been noted…

Allows for follow-up investigation in silico once correlations have been noted between pairs of protein families. SIMBAL uses clues from genomic context, such as co-occurrence or conserved gene…

UET
Dataset

UET Universal Evolutionary Trace

Provides simple and universal access to interpret protein structures and…

Provides simple and universal access to interpret protein structures and sequences in light of their evolutionary variations and divergences. UET is a repository of pre-computed evolutionary trace…

pPAP
Desktop

pPAP

Predicts the reaction of a plant type III polyketide synthases (PKS). pPAP…

Predicts the reaction of a plant type III polyketide synthases (PKS). pPAP targets PKSs acting on ring-type starter substrates, and classifies their functions into four reaction types. It is based on…

JEvTrace
Desktop

JEvTrace

A Java application implementing the evolutionary trace (ET) method and its…

A Java application implementing the evolutionary trace (ET) method and its variations. These methods have in common the analysis of protein families through MSAs, phylogenetic trees and protein…

ConSurf-DB
Dataset

ConSurf-DB

A repository for evolutionary conservation analysis of the proteins of known…

A repository for evolutionary conservation analysis of the proteins of known structures in the Protein Data Bank (PDB). Sequence homologues of each of the PDB entries were collected and aligned using…

SeSaw
Web

SeSaw Sequence-derived Structure Amignment Weights

Allows users to determine conserved sequence and structural motifs in proteins.…

Allows users to determine conserved sequence and structural motifs in proteins. SeSaw is a web application which provides a list of the templates accompanied by their corresponding annotated…

PyETV
Desktop

PyETV

A PyMOL plugin for viewing, analyzing and manipulating predictions of…

A PyMOL plugin for viewing, analyzing and manipulating predictions of evolutionarily important residues and sites in protein structures and their complexes. PyETV integrates data from several sources…

ET viewer
Desktop

ET viewer Evolutionary Trace viewer

Provides a one-stop environment in which to run, visualize and interpret…

Provides a one-stop environment in which to run, visualize and interpret evolutionary trace (ET) predictions of functional sites in protein structures. ET viewer allows a user to launch traces, and…

JAMMING
Web
Desktop

JAMMING JAva-based Multi-threaded MIN-GUI

Detects critical residues from protein structures. JAMMING may be useful in…

Detects critical residues from protein structures. JAMMING may be useful in identifying residues critical for the distinctive function of proteins even when few homologue sequences are known. Our…

VENN
Web

VENN

An interactive software application that allows users to titrate and map…

An interactive software application that allows users to titrate and map sequence conservation onto protein structures. VENN performs a type of conservation analysis that is distinct from the many…

siteFiNDER|3D
Web

siteFiNDER|3D

Conserved functional group (CFG) analysis exploits the evolutionary…

Conserved functional group (CFG) analysis exploits the evolutionary relationships present within groups of homologous proteins to identify sites that are likely to be of functional significance.…

SitesIdentify
Web

SitesIdentify

Predicts protein functional site. SitesIdentify is based on combining sequence…

Predicts protein functional site. SitesIdentify is based on combining sequence conservation information with geometry-based cleft identification. It is able to produce comparable accuracy in…

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