Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 7, Issue 8, Pages 2348-2352Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ct200237u
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Funding
- Brazilian agency CAPES
- Brazilian agency CNPq
- Brazilian agency FAPERJ
- French-Brazilian CAPES/COFECUB
- French Ministry of Foreign and European Affairs
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Describing biological macromolecular energetics from computer simulations can pose major challenges, and often necessitates enhanced conformational sampling. We describe the calculation of conformational free-energy profiles along carefully chosen collective coordinates: consensus normal modes, developed recently as robust alternatives to conventional normal modes. In an application to the HIV-1 protease, we obtain efficient sampling of significant flap opening movements governing inhibitor binding from relatively short simulations, in close correspondence with experimental results.
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