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Bioinformatics. 2011 Oct 15;27(20):2843-50. doi: 10.1093/bioinformatics/btr497. Epub 2011 Aug 27.

iMod: multipurpose normal mode analysis in internal coordinates.

Author information

1
Department of Biological Chemical Physics, Rocasolano Physical Chemistry Institute, CSIC, Serrano 119, Madrid 28006, Spain.

Abstract

MOTIVATION:

Dynamic simulations of systems with biologically relevant sizes and time scales are critical for understanding macromolecular functioning. Coarse-grained representations combined with normal mode analysis (NMA) have been established as an alternative to atomistic simulations. The versatility and efficiency of current approaches normally based on Cartesian coordinates can be greatly enhanced with internal coordinates (IC).

RESULTS:

Here, we present a new versatile tool chest to explore conformational flexibility of both protein and nucleic acid structures using NMA in IC. Consideration of dihedral angles as variables reduces the computational cost and non-physical distortions of classical Cartesian NMA methods. Our proposed framework operates at different coarse-grained levels and offers an efficient framework to conduct NMA-based conformational studies, including standard vibrational analysis, Monte-Carlo simulations or pathway exploration. Examples of these approaches are shown to demonstrate its applicability, robustness and efficiency.

CONTACT:

pablo@chaconlab.org

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
21873636
DOI:
10.1093/bioinformatics/btr497
[Indexed for MEDLINE]

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