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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 important residues and how they cluster to form functional sites.

Source text:
(Lua et al., 2016) UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures. Nucleic Acids Res.

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PyETV
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 (Evolutionary Trace (ET), PDB, PISA) and extends the trace-to-structure mapping originally implemented in the Java-based ETV to any number of structures and traces. PyETV relies on the power, flexibility and wide availability of the PyMOL molecular visualization system and its extensibility through Python. Together with other tools in the popular PyMOL viewer, PyETV provides a tool to integrate evolutionary forces into the design of experiments targeting the most functionally relevant sites of a protein.
cddApp
Supports the annotation of protein networks with information about domains and specific functional sites. cddApp is a Cytoscape module that incorporates conserved domain database (CDD) of the National Center for Biotechnology Information. It provides three main functions: (i) using the CDD Web services to search for domains in proteins in the current network, (ii) visualizing the domain annotations and (iii) linking the domain annotations to the structure through a companion app.
Fit3D
An easily accessible web application for highly accurate screening of structural motifs in 3D protein data. Such motifs play key roles in clarification of linkage between protein structure and function, which is still a demanding process. Fortunately, the comparison of three-dimensional residue patterns can aid the functional comprehension. However, there is an urgent need for up-to-date and versatile computational resources to search for local similarities. Fit3D bridges the gap between easy usability and highly accurate pattern matching.
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 linear discriminant analyses of similarity measures. The tool can detect distant paralogs of the R-4- A type. It combines two measures: one calculated by profile hidden Markov models (pHMMs) built from functionally and structurally important partial sequence regions, and the other based on mutual information between residue positions.
FlexPred
Predicts residue positions involved in conformational switches using a protein sequence alone or in combination with solvent accessibility. FlexPred is a web server that performs the prediction using: (1) sequence-derived information for a given protein sequence, or (2) sequence-derived information and solvent accessibility of residue positions for a given PDB file. The software can discover conformational switches in proteins directly trained on a large dataset of experimentally characterized examples.
VENN
Obsolete
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 programs for pairwise and multiple sequence alignments and from programs such as DALI which is used to identify proteins with similar structural folds. The ability to readily combine the vast proteomic sequence space with structural information in an automatic fashion can reveal functional attributes which have not been reported using similar tools.
JAMMING / JAva-based Multi-threaded MIN-GUI
Obsolete
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 method is divided into three steps: building networks from protein structures, tracing the shortest path connecting every pair of residues in a network, find the residues with the largest dynamic connectivity. A unique feature of this method is the inclusion of the conformational diversity of proteins in the prediction, thus reproducing a basic feature of the structure/function relationship of proteins.
SitesIdentify
Obsolete
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 predicting functional sites to its closest available counterpart, but in addition achieves improved accuracy for proteins with few characterised homologues. The tool compares favourably to other available functional site prediction tools in a comparison of methods on a non-redundant set of 237 enzymes with annotated active sites.
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