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Nucleic Acids Research 2006 34(Web Server issue):W52-W56; doi:10.1093/nar/gkl082
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© The Author 2006. Published by Oxford University Press. All rights reserved
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Article

NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis

Erik Lindahl1,2, Cyril Azuara1, Patrice Koehl3 and Marc Delarue1,*

1 Unite de Dynamique Structurale des Macromolécules, URA 2185 du C.N.R.S., Institut Pasteur 75015 Paris, France 2 Stockholm Bioinformatics Center, Stockholm University 106 91 Stockholm, Sweden 3 Computer Science Department and Genome Center, University of California Davis, CA 95616, USA

*To whom correspondence should be addressed. Tel: +33 1 45 68 86 05; Fax: +33 1 45 68 86 04; Email: delarue{at}pasteur.fr

Received February 14, 2006. Revised March 6, 2006. Accepted March 6, 2006.

Normal mode analysis (NMA) is an efficient way to study collective motions in biomolecules that bypasses the computational costs and many limitations associated with full dynamics simulations. The NOMAD-Ref web server presented here provides tools for online calculation of the normal modes of large molecules (up to 100 000 atoms) maintaining a full all-atom representation of their structures, as well as access to a number of programs that utilize these collective motions for deformation and refinement of biomolecular structures. Applications include the generation of sets of decoys with correct stereochemistry but arbitrary large amplitude movements, the quantification of the overlap between alternative conformations of a molecule, refinement of structures against experimental data, such as X-ray diffraction structure factors or Cryo-EM maps and optimization of docked complexes by modeling receptor/ligand flexibility through normal mode motions. The server can be accessed at the URL http://lorentz.immstr.pasteur.fr/nomad-ref.php.


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