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Nucleic Acids Res. 2014 Jul;42(Web Server issue):W271-6. doi: 10.1093/nar/gku339. Epub 2014 Apr 25.

iMODS: internal coordinates normal mode analysis server.

Author information

1
Department of Biological Chemical Physics, Rocasolano Physical Chemistry Institute C.S.I.C., Serrano 119, 28006 Madrid, Spain.
2
Department of Computer Science and Engineering, University Jaume I, 12071 Castellón, Spain.
3
Department of Biological Chemical Physics, Rocasolano Physical Chemistry Institute C.S.I.C., Serrano 119, 28006 Madrid, Spain pablo@chaconlab.org.

Abstract

Normal mode analysis (NMA) in internal (dihedral) coordinates naturally reproduces the collective functional motions of biological macromolecules. iMODS facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures, even with large macromolecules. The distinctive internal coordinate formulation improves the efficiency of NMA and extends its applicability while implicitly maintaining stereochemistry. Vibrational analysis, motion animations and morphing trajectories can be easily carried out at different resolution scales almost interactively. The server is versatile; non-specialists can rapidly characterize potential conformational changes, whereas advanced users can customize the model resolution with multiple coarse-grained atomic representations and elastic network potentials. iMODS supports advanced visualization capabilities for illustrating collective motions, including an improved affine-model-based arrow representation of domain dynamics. The generated all-heavy-atoms conformations can be used to introduce flexibility for more advanced modeling or sampling strategies. The server is free and open to all users with no login requirement at http://imods.chaconlab.org.

PMID:
24771341
PMCID:
PMC4086069
DOI:
10.1093/nar/gku339
[Indexed for MEDLINE]
Free PMC Article

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