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Published December 2008 | Accepted Version + Supplemental Material
Journal Article Open

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.

Additional Information

Copyright © 2008 American Chemical Society. Received May 28, 2008. Publication Date (Web): November 19, 2008. We want to thank Professor Nagarajan Vaidehi (City of Hope) and Dr. Ravinder Abrol for many insightful suggestions. We would also like to thank Mr. Caglar Tanrikulu, Mr. Peter Kekenes-Huskey, and Mr. Adam R. Griffith for testing, using, and pointing out improvements while using the software. This research was supported partially by NIH (R21-MH073910-01-A1) with additional support from DARPA-PROM. The computational facilities were provided by DURIP grants from ARO and ONR. Supporting Information: Contact information for the current SCREAM software and prediction of surface residues prior to side-chain assignment. This material is available free of charge via the Internet at http://pubs.acs.org.

Attached Files

Accepted Version - nihms86584.pdf

Supplemental Material - KAMjctc08supp.pdf

Supplemental Material - ct800196k_si_002.pdf

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Created:
August 20, 2023
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October 17, 2023