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Free Energy Profiles along Consensus Normal Modes Provide Insight into HIV-1 Protease Flap Opening
- Source :
- Journal of Chemical Theory and Computation, Journal of Chemical Theory and Computation, American Chemical Society, 2011, 7 (8), pp.2348-2352. ⟨10.1021/ct200237u⟩
- Publication Year :
- 2015
-
Abstract
- International audience; 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.
- Subjects :
- 0303 health sciences
010304 chemical physics
biology
Computer science
Sampling (statistics)
01 natural sciences
Computer Science Applications
03 medical and health sciences
HIV-1 protease
Normal mode
0103 physical sciences
biology.protein
Statistical physics
Physical and Theoretical Chemistry
[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM]
Conformational sampling
Energy (signal processing)
Simulation
030304 developmental biology
Subjects
Details
- ISSN :
- 15499618 and 15499626
- Volume :
- 7
- Issue :
- 8
- Database :
- OpenAIRE
- Journal :
- Journal of chemical theory and computation
- Accession number :
- edsair.doi.dedup.....8d67b51f05705a79b49f21130d41a226