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Nucleic Acids Research, 2003, Vol. 31, No. 13 3375-3380
© 2003 Oxford University Press

Tools for comparative protein structure modeling and analysis

Narayanan Eswar, Bino John1, Nebojsa Mirkovic1, Andras Fiser2, Valentin A. Ilyin3, Ursula Pieper, Ashley C. Stuart1, Marc A. Marti-Renom, M. S. Madhusudhan, Bozidar Yerkovich1 and Andrej Sali*

Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA USA 1 Laboratory of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, New York, USA 2 Department of Biochemistry and Seaver Foundation Center for Bioinformatics, Albert Einstein College of Medicine, New York, USA 3 Department of Biology, Northeastern University, Boston, MA, USA

*To whom correspondence should be addressed at: Mission Bay Genentech Hall, Suite N472D, 600 16th Street, University of California, San Francisco, CA 94143-2240, USA. Tel: +1 4155144227; Fax: +1 4155144231; Email: sali{at}salilab.org

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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