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Bioinformatics Advance Access originally published online on July 14, 2009
Bioinformatics 2009 25(18):2418-2424; doi:10.1093/bioinformatics/btp424
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

ADAN: a database for prediction of protein–protein interaction of modular domains mediated by linear motifs

J. A. Encinar 1,{dagger}, G. Fernandez-Ballester 1,{dagger},*, I. E. Sánchez 2, E. Hurtado-Gomez 1,3, F. Stricher 3, P. Beltrao 4 and L. Serrano 3,{ddagger}

1Instituto de Biolog{iota}a Molecular y Celular, Edificio Torregaitan, Universidad Miguel Hernandez, 03202 Elche (Alicante), Spain, 2Fundación Instituto Leloir and IIBBA-CONICET, Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina, 3EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), UPF, 08003 Barcelona, Spain and 4Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Most of the structures and functions of proteome globular domains are yet unknown. We can use high-resolution structures from different modular domains in combination with automatic protein design algorithms to predict genome-wide potential interactions of a protein. ADAN database and related web tools are online resources for the predictive analysis of ligand–domain complexes. ADAN database is a collection of different modular protein domains (SH2, SH3, PDZ, WW, etc.). It contains 3505 entries with extensive structural and functional information available, manually integrated, curated and annotated with cross-references to other databases, biochemical and thermodynamical data, simplified coordinate files, sequence files and alignments. Prediadan, a subset of ADAN database, offers position-specific scoring matrices for protein–protein interactions, calculated by FoldX, and predictions of optimum ligands and putative binding partners. Users can also scan a query sequence against selected matrices, or improve a ligand–domain interaction.

Availability: ADAN is accessible at http://adan-embl.ibmc.umh.es/ or http://adan.crg.es/.

Contact: gregorio{at}umh.es

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

{ddagger}L.S. is a ICREA professor

Associate Editor: Burkhard Rost

Received on February 13, 2009; revised on July 6, 2009; accepted on July 7, 2009

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