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Bioinformatics. 2013 Aug 15;29(16):1980-6. doi: 10.1093/bioinformatics/btt324. Epub 2013 Jun 5.

Exploration of conformational transition pathways from coarse-grained simulations.

Author information

1
Institute for Research in Biomedicine (IRB Barcelona), Joint IRB-BSC Program in Computational Biology, Baldiri Reixac 10, Barcelona, Spain.

Abstract

MOTIVATION:

A new algorithm to trace conformational transitions in proteins is presented. The method uses discrete molecular dynamics as engine to sample protein conformational space. A multiple minima Go-like potential energy function is used in combination with several enhancing sampling strategies, such as metadynamics, Maxwell Demon molecular dynamics and essential dynamics. The method, which shows an unprecedented computational efficiency, is able to trace a wide range of known experimental transitions. Contrary to simpler methods our strategy does not introduce distortions in the chemical structure of the protein and is able to reproduce well complex non-linear conformational transitions. The method, called GOdMD, can easily introduce additional restraints to the transition (presence of ligand, known intermediate, known maintained contacts, …) and is freely distributed to the community through the Spanish National Bioinformatics Institute (http://mmb.irbbarcelona.org/GOdMD).

AVAILABILITY:

Freely available on the web at http://mmb.irbbarcelona.org/GOdMD.

PMID:
23740746
DOI:
10.1093/bioinformatics/btt324
[Indexed for MEDLINE]

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