ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment
Open Access
- 19 March 2010
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 26 (9), 1160-1168
- https://doi.org/10.1093/bioinformatics/btq100
Abstract
Motivation: Exploitation of locally similar 3D patterns of physicochemical properties on the surface of a protein for detection of binding sites that may lack sequence and global structural conservation. Results: An algorithm, ProBiS is described that detects structurally similar sites on protein surfaces by local surface structure alignment. It compares the query protein to members of a database of protein 3D structures and detects with sub-residue precision, structurally similar sites as patterns of physicochemical properties on the protein surface. Using an efficient maximum clique algorithm, the program identifies proteins that share local structural similarities with the query protein and generates structure-based alignments of these proteins with the query. Structural similarity scores are calculated for the query protein's surface residues, and are expressed as different colors on the query protein surface. The algorithm has been used successfully for the detection of protein–protein, protein–small ligand and protein–DNA binding sites. Availability: The software is available, as a web tool, free of charge for academic users at http://probis.cmm.ki.si Contact:dusa@cmm.ki.si Supplementary information: Supplementary data are available at Bioinformatics online.This publication has 31 references indexed in Scilit:
- MolLoc: a web tool for the local structural alignment of molecular surfacesNucleic Acids Research, 2009
- RASMOT-3D PRO: a 3D motif search webserverNucleic Acids Research, 2009
- A survey of available tools and web servers for analysis of protein-protein interactions and interfacesBriefings in Bioinformatics, 2008
- Searching protein structure databases with DaliLite v.3Bioinformatics, 2008
- MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactionsNucleic Acids Research, 2008
- FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structuresBMC Bioinformatics, 2008
- HotSprint: database of computational hot spots in protein interfacesNucleic Acids Research, 2007
- Spatial chemical conservation of hot spot interactions in protein-protein complexesBMC Biology, 2007
- Convergent Evolution of Enzyme Active Sites Is not a Rare PhenomenonJournal of Molecular Biology, 2007
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997