Flat-Bottom Strategy for Improved Accuracy in Protein Side-Chain Placements
Victor W. T. Kam, William A. Goddard III
2008J. Chem. Theory Comput., 4(12), 2160-216950cited
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.
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Kam, V. W. T. & III, W. A. G. (2008). Flat-Bottom Strategy for Improved Accuracy in Protein Side-Chain Placements. *J. Chem. Theory Comput.*, *4*(12), 2160-2169. https://doi.org/10.1021/ct800196k