Dramatic performance enhancements for the FASTER optimization algorithm

  title={Dramatic performance enhancements for the FASTER optimization algorithm},
  author={Benjamin D. Allen and Stephen L. Mayo},
  journal={Journal of Computational Chemistry},
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… 
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Progress in computational protein design.
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Four common search techniques are studied: Monte Carlo (MC) and Monte Carlo plus quench (MCQ); genetic algorithms (GA); self-consistent mean field (SCMF); and dead-end elimination (DEE); both SCMF and MCQ perform reasonably well on core calculations, but fail considerably on the boundary calculations.
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  • Biology
    Protein science : a publication of the Protein Society
  • 1994
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