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. 2003 Jul 1;31(13):3375-80.
doi: 10.1093/nar/gkg543.

Tools for comparative protein structure modeling and analysis

Narayanan Eswar  1 , Bino John, Nebojsa Mirkovic, Andras Fiser, Valentin A Ilyin, Ursula Pieper, Ashley C Stuart, Marc A Marti-Renom, M S Madhusudhan, Bozidar Yerkovich, Andrej Sali
Affiliations

Tools for comparative protein structure modeling and analysis

Narayanan Eswar et al. Nucleic Acids Res. .

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.

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Figures

Figure 1
Figure 1
Flowchart of MODPIPE, a large-scale protein structure modeling pipeline. See text for details.
See this image and copyright information in PMC

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