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. doi:10.1021/ct800196k. 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:

URL	URL Type	Description
http://dx.doi.org/10.1021/ct800196k	DOI	Article
http://pubs.acs.org/doi/abs/10.1021/ct800196k	Publisher	Article
http://pubs.acs.org/doi/suppl/10.1021/ct800196k	Publisher	Supporting Information
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4692055	PubMed Central	Article

ORCID:

Author	ORCID
Goddard, William A., III	0000-0003-0097-5716

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 Agency	Grant Number
NIH	R21-MH073910-01-A1
Defense Advanced Research Projects Agency (DARPA)	UNSPECIFIED
Army Research Office (ARO)	UNSPECIFIED
Office of Naval Research (ONR)	UNSPECIFIED

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PubMed Central ID:

PMC4692055

DOI:

10.1021/ct800196k

Record Number:

CaltechAUTHORS:KAMjctc08

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https://resolver.caltech.edu/CaltechAUTHORS:KAMjctc08

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No commercial reproduction, distribution, display or performance rights in this work are provided.

ID Code:

12856

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CaltechAUTHORS

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Deposited On:

08 Jan 2009 21:53

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08 Nov 2021 22:33

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