Literature DB >> 26620487

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

Victor Wai Tak Kam1, William A Goddard1.   

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.

Entities:  

Year:  2008        PMID： 26620487      PMCID： PMC4692055          DOI： 10.1021/ct800196k

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN： 1549-9618            Impact factor:   6.006


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