Nucleic Acids Research Advance Access originally published online on October 23, 2008
Nucleic Acids Research 2009 37(Database issue):D347-D354; doi:10.1093/nar/gkn791
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Nucleic Acids Research, 2009, Vol. 37, Database issue D347-D354
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
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MODBASE, a database of annotated comparative protein structure models and associated resources
1Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, 2Graduate Group in Biophysics, 3Graduate Group in Bioinformatics, University of California at San Francisco, CA, 4Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA, 5Structural Genomics Unit, Bioinformatics & Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Avda. Autopista del Saler 16, Valencia 46012, Spain and 6Howard Hughes Medical Institute, Janelia Farm, 19700 Helix Drive, Ashburn, VA 20147, USA
*To whom correspondence should be addressed. Tel: +1 415 514 4227; Fax: +1 415 514 4231; Email: sali{at}salilab.org
Received September 15, 2008. Accepted October 8, 2008.
MODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by MODPIPE, an automated modeling pipeline that relies primarily on MODELLER for fold assignment, sequence–structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE currently contains 5 152 695 reliable models for domains in 1 593 209 unique protein sequences; only models based on statistically significant alignments and/or models assessed to have the correct fold are included. MODBASE also allows users to calculate comparative models on demand, through an interface to the MODWEB modeling server (http://salilab.org/modweb). Other resources integrated with MODBASE include databases of multiple protein structure alignments (DBAli), structurally defined ligand binding sites (LIGBASE), predicted ligand binding sites (AnnoLyze), structurally defined binary domain interfaces (PIBASE) and annotated single nucleotide polymorphisms and somatic mutations found in human proteins (LS-SNP, LS-Mut). MODBASE models are also available through the Protein Model Portal (http://www.proteinmodelportal.org/).
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