Flat-Bottom Strategy for Improved Accuracy in Protein Side-Chain Placements.

ABSTRACT: 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 Excitation Analysis Method is implemented in the SCREAM software package. Similar scoring function strategies should be useful for ligand docking, virtual ligand screening, and protein folding applications.

SUBMITTER: Tak Kam VW 

PROVIDER: S-EPMC4692055 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature