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    Polarizable protein packing

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    Type
    Article
    Authors
    Ng, Albert H.
    Snow, Christopher D.
    KAUST Grant Number
    KUS-F1-028-03
    Date
    2011-01-24
    Online Publication Date
    2011-01-24
    Print Publication Date
    2011-05
    Permanent link to this record
    http://hdl.handle.net/10754/599205
    
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    Abstract
    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
    Wiley
    Journal
    Journal of Computational Chemistry
    DOI
    10.1002/jcc.21714
    PubMed ID
    21264879
    ae974a485f413a2113503eed53cd6c53
    10.1002/jcc.21714
    Scopus Count
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