Journal Article

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

J. A. Encinar, G. Fernandez-Ballester, I. E. Sánchez, E. Hurtado-Gomez, F. Stricher, P. Beltrao and L. Serrano

in Bioinformatics

Volume 25, issue 18, pages 2418-2424
Published in print September 2009 | ISSN: 1367-4803
Published online July 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp424
ADAN: a database for prediction of protein–protein interaction of modular domains mediated by linear motifs

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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@umh.es

Journal Article.  6040 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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