KAUST Grant NumberKUS-F1-028-03
Online Publication Date2011-01-24
Print Publication Date2011-05
Permanent link to this recordhttp://hdl.handle.net/10754/599205
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AbstractTo incorporate protein polarization effects within a protein combinatorial optimization framework, we decompose the polarizable force field AMOEBA into low order terms. Including terms up to the third-order provides a fair approximation to the full energy while maintaining tractability. We represent the polarizable packing problem for protein G as a hypergraph and solve for optimal rotamers with the FASTER combinatorial optimization algorithm. These approximate energy models can be improved to high accuracy [root mean square deviation (rmsd) < 1 kJ mol -1] via ridge regression. The resulting trained approximations are used to efficiently identify new, low-energy solutions. The approach is general and should allow combinatorial optimization of other many-body problems. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011 Copyright © 2011 Wiley Periodicals, Inc.
CitationNg AH, Snow CD (2011) Polarizable protein packing. Journal of Computational Chemistry 32: 1334–1344. Available: http://dx.doi.org/10.1002/jcc.21714.
SponsorsContract/grant sponsor: King Abdullah University of Science and Technology (KAUST); contract/grant numbers: KUS-F1-028-03The authors thank Frances H. Arnold for support. The authors thank Phillip A. Romero, Gevorg Grigoryan, and an anonymous reviewer for useful suggestions. A.H.N. was supported by the Caltech Summer Undergraduate Research Fellowship program (SURF).
CollectionsPublications Acknowledging KAUST Support
- Dramatic performance enhancements for the FASTER optimization algorithm.
- Authors: Allen BD, Mayo SL
- Issue date: 2006 Jul 30
- Modeling side-chain conformation for homologous proteins using an energy-based rotamer search.
- Authors: Wilson C, Gregoret LM, Agard DA
- Issue date: 1993 Feb 20
- A new force field (ECEPP-05) for peptides, proteins, and organic molecules.
- Authors: Arnautova YA, Jagielska A, Scheraga HA
- Issue date: 2006 Mar 16
- Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations.
- Authors: Mackerell AD Jr, Feig M, Brooks CL 3rd
- Issue date: 2004 Aug
- Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions.
- Authors: Olson MA, Feig M, Brooks CL 3rd
- Issue date: 2008 Apr 15