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© Structural Dynamics Of Macromolecules
The structure of a bacterial analog of the nicotinic receptor (one color per subunit) inserted into the cell membrane (grey and orange). A representation of the volume accessible to ions is shown in yellow.
Publication : Nucleic acids research

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

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Nucleic acids research - 01 Jul 2006

Lindahl E, Azuara C, Koehl P, Delarue M

Link to Pubmed [PMID] – 16845062

Nucleic Acids Res. 2006 Jul;34(Web Server issue):W52-6

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.

https://www.ncbi.nlm.nih.gov/pubmed/16845062