PICCOLO


21801404	Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database. [PMID: 21801404] Bickerton GR, Higueruelo AP, Blundell TL. Abstract BACKGROUND: Structural 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. RESULTS: Here 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. CONCLUSIONS: The 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. BMC Bioinformatics. 2011:12() \| 35 Citations (from Europe PMC, 2025-03-29)

Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database. [PMID: 21801404]

Bickerton GR, Higueruelo AP, Blundell TL.

Abstract

BACKGROUND: Structural 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.
RESULTS: Here 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.
CONCLUSIONS: The 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.

BMC Bioinformatics. 2011:12() | 35 Citations (from Europe PMC, 2025-03-29)

URL:	http://www-cryst.bioc.cam.ac.uk/piccolo
Full name:
Description:	Here 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.
Year founded:	2011
Last update:
Version:
Accessibility:	Unaccessible
Country/Region:	United Kingdom

Data type:	Protein
Data object:	Animal Archaea Bacteria Fungi Plant Virus
Database category:	Interaction
Major species:	NA
Keywords:	Comprehensive atomic-level characterization of structurally characterized protein-protein interactions

University/Institution:	University of Cambridge
Address:	Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
City:	Cambridge
Province/State:
Country/Region:	United Kingdom
Contact name (PI/Team):	Bickerton GR
Contact email (PI/Helpdesk):	grbickerton@dundee.ac.uk

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Database Commons a catalog of worldwide biological databases