Flat-Bottom Strategy for Improved Accuracy in Protein Side-Chain Placements.
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ABSTRACT:
SUBMITTER: Tak Kam VW
PROVIDER: S-EPMC4692055 | biostudies-literature | 2008 Dec
REPOSITORIES: biostudies-literature
Publications
Flat-Bottom Strategy for Improved Accuracy in Protein Side-Chain Placements.
Tak Kam Victor Wai VW Goddard William A WA
Journal of chemical theory and computation 20081201 12
We present a new strategy for protein side-chain placement that uses flat-bottom potentials for rotamer scoring. The extent of the flat bottom depends on the coarseness of the rotamer library and is optimized for libraries ranging from diversities of 0.2 Å to 5.0 Å. The parameters reported here were optimized for forcefields using Lennard-Jones 12-6 van der Waals potential with DREIDING parameters but are expected to be similar for AMBER, CHARMM, and other forcefields. This Side-Chain Rotamer Ex ...[more]
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