Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database

BMC Bioinformatics

Research Article

Alicia P Higueruelo¹  Tom L Blundell¹  George R Bickerton² 

[1] Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK;Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK;Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Dundee, UK;

关键词: Solvent Accessibility;    Accessible Surface Area;    Residue Type;    Protein Interface;    Contact Preference;   

DOI  :  10.1186/1471-2105-12-313

 received in 2011-02-04, accepted in 2011-07-29,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundStructural studies are increasingly providing huge amounts of information on multi-protein assemblies. Although a complete understanding of cellular processes will be dependent on an explicit characterization of the intermolecular interactions that underlie these assemblies and mediate molecular recognition, these are not well described by standard representations.ResultsHere we present PICCOLO, a comprehensive relational database capturing the details of structurally characterized protein-protein interactions. Interactions are described at the level of interacting pairs of atoms, residues and polypeptide chains, with the physico-chemical nature of the interactions being characterized. Distance and angle terms are used to distinguish 12 different interaction types, including van der Waals contacts, hydrogen bonds and hydrophobic contacts. The explicit aim of PICCOLO is to underpin large-scale analyses of the properties of protein-protein interfaces. This is exemplified by an analysis of residue propensity and interface contact preferences derived from a much larger data set than previously reported. However, PICCOLO also supports detailed inspection of particular systems of interest.ConclusionsThe current PICCOLO database comprises more than 260 million interacting atom pairs from 38,202 protein complexes. A web interface for the database is available at http://www-cryst.bioc.cam.ac.uk/piccolo.

【 授权许可】

CC BY   
© Bickerton et al; licensee BioMed Central Ltd. 2011