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Nucleic Acids Research 2006 34(Database Issue):D291-D295; doi:10.1093/nar/gkj059
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Nucleic Acids Research, 2006, Vol. 34, Database issue D291-D295
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

MODBASE: a database of annotated comparative protein structure models and associated resources

Ursula Pieper1,2, Narayanan Eswar1,2, Fred P. Davis1,2, Hannes Braberg1,2, M. S. Madhusudhan1,2, Andrea Rossi1,2, Marc Marti-Renom1,2, Rachel Karchin1,2, Ben M. Webb1,2, David Eramian1,2,4, Min-Yi Shen1,2, Libusha Kelly1,2,5, Francisco Melo3 and Andrej Sali1,2,*

1Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research QB3 at Mission Bay, Office 503B University of California at San Francisco 1700 4th Street, San Francisco, CA 94158, USA 2Department Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Research QB3 at Mission Bay, Office 503B University of California at San Francisco 1700 4th Street, San Francisco, CA 94158, USA 3Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile Alameda 340, Santiago, Chile 4Graduate Group in Biophysics, University of California San Francisco, CA, USA 5Graduate Group in Biological and Medical Informatics, University of California San Francisco, CA, USA

*To whom correspondence should be addressed. Tel: +1 415 514 4227; Fax: +1 415 514 4231; Email: sali{at}salilab.org

Received September 14, 2005. Accepted October 5, 2005.

MODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models for all available protein sequences that can be matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on MODELLER for fold assignment, sequence–structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, and improvements in the software for calculating the models. MODBASE currently contains 3 094 524 reliable models for domains in 1 094 750 out of 1 817 889 unique protein sequences in the UniProt database (July 5, 2005); only models based on statistically significant alignments and models assessed to have the correct fold despite insignificant alignments are included. MODBASE also allows users to generate comparative models for proteins of interest with the automated modeling server MODWEB (http://salilab.org/modweb). Our other resources integrated with MODBASE include comprehensive databases of multiple protein structure alignments (DBAli, http://salilab.org/dbali), structurally defined ligand binding sites and structurally defined binary domain interfaces (PIBASE, http://salilab.org/pibase) as well as predictions of ligand binding sites, interactions between yeast proteins, and functional consequences of human nsSNPs (LS-SNP, http://salilab.org/LS-SNP).


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