DOI: 10.1002/jcc.10083. Modern protein force fields behave comparably in molecular dynamics simulations

Modern protein force fields behave comparably in molecular dynamics simulations

10.1002/jcc.10083

Crossref journal-article

Wiley

Journal of Computational Chemistry (311)

Abstract

AbstractSeveral molecular dynamics simulations were performed on three proteins—bovine apo‐calbindin D9K, human interleukin‐4 R88Q mutant, and domain IIA of bacillus subtilis glucose permease—with each of the AMBER94, CHARMM22, and OPLS‐AA force fields as implemented in CHARMM. Structural and dynamic properties such as solvent‐accessible surface area, radius of gyration, deviation from their respective experimental structures, secondary structure, and backbone order parameters are obtained from each of the 2‐ns simulations for the purpose of comparing the protein portions of these force fields. For one of the proteins, the interleukin‐4 mutant, two independent simulations were performed using the CHARMM22 force field to gauge the sensitivity of some of these properties to the specific trajectory. In general, the force fields tested performed remarkably similarly with differences on the order of those found for the two independent trajectories of interleukin‐4 with CHARMM22. When all three proteins are considered together, no force field showed any consistent trend in variations for most of the properties monitored in the study. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1045–1057, 2002

Bibliography

Price, D. J., & Brooks, C. L. (2002). Modern protein force fields behave comparably in molecular dynamics simulations. Journal of Computational Chemistry, 23(11), 1045â1057. Portico.

Authors 2

Daniel J. Price (first)
Charles L. Brooks (additional)

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Dates

Type	When
Created	22 years, 11 months ago (Oct. 6, 2002, 8:29 a.m.)
Deposited	1 year, 10 months ago (Oct. 17, 2023, 8:39 a.m.)
Indexed	4 days, 7 hours ago (Sept. 3, 2025, 6:18 a.m.)
Issued	23 years, 3 months ago (May 31, 2002)
Published	23 years, 3 months ago (May 31, 2002)
Published Online	23 years, 3 months ago (May 31, 2002)
Published Print	23 years, 1 month ago (Aug. 1, 2002)

Funders 0

None

BibTeX

@article{Price_2002, title={Modern protein force fields behave comparably in molecular dynamics simulations}, volume={23}, ISSN={1096-987X}, url={http://dx.doi.org/10.1002/jcc.10083}, DOI={10.1002/jcc.10083}, number={11}, journal={Journal of Computational Chemistry}, publisher={Wiley}, author={Price, Daniel J. and Brooks, Charles L.}, year={2002}, month=may, pages={1045–1057} }

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