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Binding-site similarity identification software tools | Protein structure data analysis

Detection of ligand-binding sites in protein structures is a crucial task in structural bioinformatics, and has applications in important areas like drug discovery. Given the knowledge of the site in a particular protein structure that binds to a…
ProBis
Web

ProBis Protein Binding Sites

Helps for prediction and study of protein binding sites and their ligands.…

Helps for prediction and study of protein binding sites and their ligands. ProBiS provides algorithm, database, and web servers based on graph theoretical approaches combined with molecular…

IsoMIF Finder
Desktop
Web

IsoMIF Finder

An online server for the identification of molecular interaction field (MIF)…

An online server for the identification of molecular interaction field (MIF) similarities. User defined binding site MIFs can be compared to datasets of pre-calculated MIFs or against a user-defined…

FTProd
Desktop

FTProd binding site comparison across multiple structures

Eases identification and characterization of hot spots spanning multiple…

Eases identification and characterization of hot spots spanning multiple structures. FTProd analyzes structures which contain a series of small molecular probes indicating the location of potentially…

GenProBiS
Web

GenProBiS

Maps sequence variants to protein structures from the Protein Data Bank (PDB),…

Maps sequence variants to protein structures from the Protein Data Bank (PDB), and further to protein–protein, protein–nucleic acid, protein–compound, and protein–metal ion binding sites.…

eMatchSite
Desktop
Web

eMatchSite

Allows alignment and matching for ligand binding site. eMatchSite accurately…

Allows alignment and matching for ligand binding site. eMatchSite accurately identifies pairs of pockets that bind similar compounds even in proteins with different global structures. Furthermore, it…

PESDserv
Web

PESDserv

Allows high-throughput protein binding site comparison. PESDserv is a…

Allows high-throughput protein binding site comparison. PESDserv is a web-server that implements the property encoded shape distributions (PESD) algorithm and allows fast web-based global similarity…

SiteEngine
Web

SiteEngine

Predicts regions that can potentially function as binding sites. The method is…

Predicts regions that can potentially function as binding sites. The method is based on recognition of geometrical and physico-chemical environments that are similar to known binding sites.

pdbFun
Web

pdbFun

A web server for structural and functional analysis of proteins at the residue…

A web server for structural and functional analysis of proteins at the residue level. pdbFun gives fast access to the whole Protein Data Bank (PDB) organized as a database of annotated residues. The…

SIENA
Web

SIENA

Creates protein-structural ensembles for the analysis of protein flexibility,…

Creates protein-structural ensembles for the analysis of protein flexibility, molecular design efforts like docking or de novo design within seconds. SIENA is an online pipeline that permits to…

SuMo
Web

SuMo

A bioinformatic system for finding similarities in arbitrary 3D structures or…

A bioinformatic system for finding similarities in arbitrary 3D structures or substructures of proteins. SuMo is based on a unique representation of macromolecules using selected triplets of chemical…

APoc
Desktop

APoc Alignment of Pockets

A computational method for the large-scale, sequence order-independent,…

A computational method for the large-scale, sequence order-independent, structural comparison of protein pockets. A scoring function, the Pocket Similarity Score (PS-score), is derived to measure the…

PocketAlign
Web
Desktop

PocketAlign

A software to obtain structural superpositions of binding sites. PocketAlign…

A software to obtain structural superpositions of binding sites. PocketAlign encodes shape descriptors in the form of geometric perspectives, supplemented by chemical group classification of the…

BsFinder
Desktop

BsFinder

Identifies regions of binding sites on the proteins. BsFinder first proceeds to…

Identifies regions of binding sites on the proteins. BsFinder first proceeds to a local sequence alignment then detects protein surface, and finally compares 3d structures. The software can perform…

PARIS
Desktop

PARIS Pocket Alignment in Relation to Identification of Substrates

A method to measure the similarity between protein binding sites. In this…

A method to measure the similarity between protein binding sites. In this method, binding pockets are described as clouds of points in the 3D space, each point corresponding to an atom. These points…

PocketMatch
Web

PocketMatch

An algorithm for comparison of binding sites in a frame invariant manner. Each…

An algorithm for comparison of binding sites in a frame invariant manner. Each binding site is represented by 90 lists of sorted distances capturing shape and chemical nature of the site. The sorted…

BSAlign
Desktop

BSAlign Binding Site Aligner

A method for rapid detection of potential binding site(s) in the target…

A method for rapid detection of potential binding site(s) in the target protein(s) that is/are similar to the query protein's ligand-binding site. We represent both the binding site and the…

IsoCleft Finder
Web

IsoCleft Finder

A web-based tool for the detection of local geometric and chemical similarities…

A web-based tool for the detection of local geometric and chemical similarities between potential small-molecule binding cavities and a non-redundant dataset of ligand-bound known small-molecule…

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