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

Kam, Victor Wai Tak and Goddard, William A., III (2008) Flat-Bottom Strategy for Improved Accuracy in Protein Side-Chain Placements. Journal of Chemical Theory and Computation, 4 (12). pp. 2160-2169. ISSN 1549-9626. PMCID PMC4692055. https://resolver.caltech.edu/CaltechAUTHORS:KAMjctc08

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1021/ct800196kDOIArticle
http://pubs.acs.org/doi/abs/10.1021/ct800196kPublisherArticle
http://pubs.acs.org/doi/suppl/10.1021/ct800196kPublisherSupporting Information
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4692055PubMed CentralArticle
ORCID:
AuthorORCID
Goddard, William A., III0000-0003-0097-5716
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.
Funders:
Funding AgencyGrant Number
NIHR21-MH073910-01-A1
Defense Advanced Research Projects Agency (DARPA)UNSPECIFIED
Army Research Office (ARO)UNSPECIFIED
Office of Naval Research (ONR)UNSPECIFIED
Issue or Number:12
PubMed Central ID:PMC4692055
Record Number:CaltechAUTHORS:KAMjctc08
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:KAMjctc08
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:12856
Collection:CaltechAUTHORS
Deposited By: Archive Administrator
Deposited On:08 Jan 2009 21:53
Last Modified:26 Nov 2019 11:15

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