Nucleic Acids Research Advance Access published online on October 30, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp893
Database Issue |
PepX: a structural database of non-redundant protein–peptide complexes
1VIB SWITCH Laboratory, 2Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium, 3EMBL-CRG Systems Biology Unit, CRG-Centre de Regulacio Genomica, Dr Aiguader 88, 08003 Barcelona and 4ICREA. Institucio Catala de Recerca i Estudis Avancats. Passeig Lluís Companys, 23 08010 Barcelona, Spain
*To whom correspondence should be addressed. Tel: +32 2 629 14 25; Fax: +32 2 629 19 63; Email: joost.schymkowitz{at}switch.vib-vub.be
Correspondence may also be addressed to Frederic Rousseau. Email: frederic.rousseau{at}switch.vib-vub.be
Received August 15, 2009. Revised October 1, 2009. Accepted October 6, 2009.
Although protein–peptide interactions are estimated to constitute up to 40% of all protein interactions, relatively little information is available for the structural details of these interactions. Peptide-mediated interactions are a prime target for drug design because they are predominantly present in signaling and regulatory networks. A reliable data set of nonredundant protein–peptide complexes is indispensable as a basis for modeling and design, but current data sets for protein–peptide interactions are often biased towards specific types of interactions or are limited to interactions with small ligands. In PepX (http://pepx.switchlab.org), we have designed an unbiased and exhaustive data set of all protein–peptide complexes available in the Protein Data Bank with peptide lengths up to 35 residues. In addition, these complexes have been clustered based on their binding interfaces rather than sequence homology, providing a set of structurally diverse protein–peptide interactions. The final data set contains 505 unique protein–peptide interface clusters from 1431 complexes. Thorough annotation of each complex with both biological and structural information facilitates searching for and browsing through individual complexes and clusters. Moreover, we provide an additional source of data for peptide design by annotating peptides with naturally occurring backbone variations using fragment clusters from the BriX database.