Welcome to the new version of CaltechAUTHORS. Login is currently restricted to library staff. If you notice any issues, please email coda@library.caltech.edu
Published July 30, 2006 | public
Journal Article

Dramatic performance enhancements for the FASTER optimization algorithm


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.

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.

Additional details

August 22, 2023
October 24, 2023