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NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis
Stockholm University.ORCID iD: 0000-0002-2734-2794
Institut Pasteur, Paris France.
Institut Pasteur, Paris France.
2006 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 34, no SI, W52-W56 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2006. Vol. 34, no SI, W52-W56 p.
National Category
Biophysics Theoretical Chemistry
Identifiers
URN: urn:nbn:se:kth:diva-82627DOI: 10.1093/nar/gkl082ISI: 000245650200012PubMedID: 16845062OAI: oai:DiVA.org:kth-82627DiVA: diva2:498435
Note
QC 20120227Available from: 2012-02-12 Created: 2012-02-12 Last updated: 2017-12-07Bibliographically approved

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Lindahl, Erik

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