Type
ArticleKAUST Grant Number
KUS-F1-028-03Date
2011-01-24Online Publication Date
2011-01-24Print Publication Date
2011-05Permanent link to this record
http://hdl.handle.net/10754/599205
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To 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.Citation
Ng AH, Snow CD (2011) Polarizable protein packing. Journal of Computational Chemistry 32: 1334–1344. Available: http://dx.doi.org/10.1002/jcc.21714.Sponsors
Contract/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).Publisher
WileyPubMed ID
21264879ae974a485f413a2113503eed53cd6c53
10.1002/jcc.21714
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