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Dramatic performance enhancements for the FASTER optimization algorithm

Allen, Benjamin D. and Mayo, Stephen L. (2006) Dramatic performance enhancements for the FASTER optimization algorithm. Journal of Computational Chemistry, 27 (10). pp. 1071-1075. ISSN 0192-8651. doi:10.1002/jcc.20420.

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FASTER is a combinatorial optimization algorithm useful for finding low-energy side-chain configurations in side-chain placement and protein design calculations. We present two simple enhancements to FASTER that together improve the computational efficiency of these calculations by as much as two orders of magnitude with no loss of accuracy. Our results highlight the importance of choosing appropriate initial configurations, and show that efficiency can be improved by stringently limiting the number of positions that are allowed to relax in response to a perturbation. The changes we describe improve the quality of solutions found for large-scale designs, and allow them to be found in hours rather than days. The improved FASTER algorithm finds low-energy solutions more efficiently than common optimization schemes based on the dead-end elimination theorem and Monte Carlo. These advances have prompted investigations into new methods for force field parameterization and multiple state design.

Item Type:Article
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URLURL TypeDescription
Allen, Benjamin D.0000-0001-6914-5572
Mayo, Stephen L.0000-0002-9785-5018
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Additional Information:© 2006 Wiley Periodicals, Inc. Received 18 November 2005; Accepted 16 January 2006; Article first published online: 9 May 2006. Contract/grant sponsor: Howard Hughes Medical Institute (S.L.M.). Contract/grant sponsor: Ralph M. Parsons Foundation (S.L.M.) Contract/grant sponsor: IBM Shared University Research Grant (S.L.M.) We thank Marie Ary and Christina Vizcarra for critical review of this manuscript.
Funding AgencyGrant Number
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Ralph M. Parsons FoundationUNSPECIFIED
Subject Keywords:protein design; side-chain placement; combinatorial optimization; FASTER; Monte Carlo
Issue or Number:10
Record Number:CaltechAUTHORS:20110913-165232651
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Official Citation:Allen, B. D. and Mayo, S. L. (2006), Dramatic performance enhancements for the FASTER optimization algorithm. Journal of Computational Chemistry, 27: 1071–1075. doi: 10.1002/jcc.20420
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:25327
Deposited By: Marie Ary
Deposited On:15 Sep 2011 16:57
Last Modified:09 Nov 2021 16:32

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