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

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...

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Bibliographic Details
Published in:Nucleic acids research 2006-07, Vol.34 (suppl-2), p.W52-W56
Main Authors: Lindahl, Erik, Azuara, Cyril, Koehl, Patrice, Delarue, Marc
Format: Article
Language:English
Subjects:
biochemical compounds
Biochemistry, Molecular Biology
Computer Graphics
computer software
deformation
dynamics
Internet
Internet resource
Life Sciences
Ligands
Macromolecular Substances
Macromolecular Substances - chemistry
Models, Molecular
molecular models
Molecular Structure
Motion
optimization
Proteins
Proteins - chemistry
quantitative analysis
receptors
Software
stereochemistry
X-radiation
X-ray diffraction
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Description
Summary: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.
ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gkl082