期刊
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
卷 7, 期 8, 页码 2348-2352出版社
AMER CHEMICAL SOC
DOI: 10.1021/ct200237u
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资金
- Brazilian agency CAPES
- Brazilian agency CNPq
- Brazilian agency FAPERJ
- French-Brazilian CAPES/COFECUB
- French Ministry of Foreign and European Affairs
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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