Nucleic Acids Res. 2003 Jul 1;31(13):3375-80.

Tools for comparative protein structure modeling and analysis.

Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, Madhusudhan MS, Yerkovich B, Sali A.

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Department of Biopharmaceutical Sciences and California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94143-2240, USA.

Abstract

The following resources for comparative protein structure modeling and analysis are described (http://salilab.org): MODELLER, a program for comparative modeling by satisfaction of spatial restraints; MODWEB, a web server for automated comparative modeling that relies on PSI-BLAST, IMPALA and MODELLER; MODLOOP, a web server for automated loop modeling that relies on MODELLER; MOULDER, a CPU intensive protocol of MODWEB for building comparative models based on distant known structures; MODBASE, a comprehensive database of annotated comparative models for all sequences detectably related to a known structure; MODVIEW, a Netscape plugin for Linux that integrates viewing of multiple sequences and structures; and SNPWEB, a web server for structure-based prediction of the functional impact of a single amino acid substitution.

PMID:: 12824331; [PubMed - indexed for MEDLINE]
PMCID:: PMC168950

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MODBASE, a database of annotated comparative protein structure models, and associated resources. [Nucleic Acids Res. 2004]
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Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, et al. Nucleic Acids Res. 2004 Jan 1; 32(Database issue):D217-22.
MODBASE: a database of annotated comparative protein structure models and associated resources. [Nucleic Acids Res. 2006]
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