MODELLER
PROTEIN MODELING BY SATISFACTION OF SPATIAL RESTRAINTS

Copyright(©) 1989-2007 Andrej Sali
All Rights Reserved

Written by Andrej Sali
University of California San Francisco, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK

Contact: Andrej Sali, Mission Bay, Byers Hall,
1700 4th Street, Suite 503B,
University of California, San Francisco,
San Francisco, CA 94158-2330, USA.
Tel +1 (415) 514-4227
Fax +1 (415) 514-4231
Email: modeller-care@salilab.org

DESCRIPTION

MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1,2). The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints (3,4), and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. MODELLER is available for download for most Unix/Linux systems, Windows, and Mac.

1. N. Eswar, D. Eramian, B. Webb, M. Shen, A. Sali. Protein Structure Modeling With MODELLER. Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006

2. M.A. Marti-Renom, A. Stuart, A. Fiser, R. S=E1nchez, F. Melo, A. Sali. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291-325, 2000.

3. A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993.

4. A. Fiser, R.K. Do, & A. Sali. Modeling of loops in protein structures, Protein Science 9. 1753-1773, 2000.

AVAILABILITY

MODELLER is available free of charge to academic non-profit institutions. For governmental or commercial licensing of MODELLER, please contact Mrs. Dana Haley-Vicente, Ph.D., at Accelrys Inc., 10188 Telesis Ct. Suite 100, San Diego, CA 92121, USA, tel +1 (858) 799-5322, fax +1 (858) 799-5100, email dhv@accelrys.com, web http://www.accelrys.com/. Several graphical interfaces to MODELLER are commercially available from Accelrys. Teaching licenses are also available to those institutions that acquire and maintain a research license.

DOWNLOAD

To obtain the MODELLER program, please visit the website at http://salilab.org/modeller/. You can also contact Ben Webb, the Modeller Caretaker at modeller-care@salilab.org. The Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage.



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