DOI: 10.1002/prot.10001. Evaluation of a fast implicit solvent model for molecular dynamics simulations

Evaluation of a fast implicit solvent model for molecular dynamics simulations

10.1002/prot.10001

Crossref journal-article

Wiley

Proteins: Structure, Function, and Bioinformatics (311)

Abstract

AbstractA solvation term based on the solvent accessible surface area (SASA) is combined with the CHARMM polar hydrogen force field for the efficient simulation of peptides and small proteins in aqueous solution. Only two atomic solvation parameters are used: one is negative for favoring the direct solvation of polar groups and the other positive for taking into account the hydrophobic effect on apolar groups. To approximate the water screening effects on the intrasolute electrostatic interactions, a distance‐dependent dielectric function is used and ionic side chains are neutralized. The use of an analytical approximation of the SASA renders the model extremely efficient (i.e., only about 50% slower than in vacuo simulations). The limitations and range of applicability of the SASA model are assessed by simulations of proteins and structured peptides. For the latter, the present study and results reported elsewhere show that with the SASA model it is possible to sample a significant amount of folding/unfolding transitions, which permit the study of the thermodynamics and kinetics of folding at an atomic level of detail. Proteins 2002;46:24–33. © 2001 Wiley‐Liss, Inc.

Bibliography

Ferrara, P., Apostolakis, J., & Caflisch, A. (2001). Evaluation of a fast implicit solvent model for molecular dynamics simulations. Proteins: Structure, Function, and Bioinformatics, 46(1), 24â33. Portico.

Authors 3

Philippe Ferrara (first)
Joannis Apostolakis (additional)
Amedeo Caflisch (additional)

References 50 Referenced 276

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Dates

Type	When
Created	22 years, 11 months ago (Sept. 9, 2002, 3:37 p.m.)
Deposited	1 year, 10 months ago (Oct. 7, 2023, 7:18 p.m.)
Indexed	1 month ago (July 30, 2025, 11:26 a.m.)
Issued	23 years, 9 months ago (Nov. 15, 2001)
Published	23 years, 9 months ago (Nov. 15, 2001)
Published Online	23 years, 9 months ago (Nov. 15, 2001)
Published Print	23 years, 8 months ago (Jan. 1, 2002)

Funders 0

None

BibTeX

@article{Ferrara_2001, title={Evaluation of a fast implicit solvent model for molecular dynamics simulations}, volume={46}, ISSN={1097-0134}, url={http://dx.doi.org/10.1002/prot.10001}, DOI={10.1002/prot.10001}, number={1}, journal={Proteins: Structure, Function, and Bioinformatics}, publisher={Wiley}, author={Ferrara, Philippe and Apostolakis, Joannis and Caflisch, Amedeo}, year={2001}, month=nov, pages={24–33} }

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