Handle URI:
http://hdl.handle.net/10754/599205
Title:
Polarizable protein packing
Authors:
Ng, Albert H.; Snow, Christopher D.
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.
Publisher:
Wiley-Blackwell
Journal:
Journal of Computational Chemistry
KAUST Grant Number:
KUS-F1-028-03
Issue Date:
24-Jan-2011
DOI:
10.1002/jcc.21714
PubMed ID:
21264879
Type:
Article
ISSN:
0192-8651
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).
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorNg, Albert H.en
dc.contributor.authorSnow, Christopher D.en
dc.date.accessioned2016-02-25T13:54:52Zen
dc.date.available2016-02-25T13:54:52Zen
dc.date.issued2011-01-24en
dc.identifier.citationNg AH, Snow CD (2011) Polarizable protein packing. Journal of Computational Chemistry 32: 1334–1344. Available: http://dx.doi.org/10.1002/jcc.21714.en
dc.identifier.issn0192-8651en
dc.identifier.pmid21264879en
dc.identifier.doi10.1002/jcc.21714en
dc.identifier.urihttp://hdl.handle.net/10754/599205en
dc.description.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.en
dc.description.sponsorshipContract/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).en
dc.publisherWiley-Blackwellen
dc.subjectAMOEBAen
dc.subjectpolarizable force fielden
dc.subjectprotein structure predictionen
dc.subjectridge regressionen
dc.subjectrotamer optimizationen
dc.titlePolarizable protein packingen
dc.typeArticleen
dc.identifier.journalJournal of Computational Chemistryen
dc.contributor.institutionCalifornia Institute of Technology, Pasadena, United Statesen
kaust.grant.numberKUS-F1-028-03en

Related articles on PubMed

All Items in KAUST are protected by copyright, with all rights reserved, unless otherwise indicated.