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Cited by 4,441

The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.

A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations

Duan, Yong, Wu, Chun, Chowdhury, Shibasish, Lee, Mathew C., Xiong, Guoming, Zhang, Wei, Yang, Rong, Cieplak, Piotr, Luo, Ray, Lee, Taisung, Caldwell, James, Wang, Junmei, Kollman, Peter·2003·Journal of Computational Chemistry
DOI 10.1002/jcc.10349
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Abstract

Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third‐generation point‐charge all‐atom force field for proteins. Following the earlier approach of Cornell et al., the charge set was obtained by fitting to the electrostatic potentials of dipeptides calculated using B3LYP/cc‐pVTZ//HF/6‐31G** quantum mechanical methods. The main‐chain torsion parameters were obtained by fitting to the energy profiles of Ace‐Ala‐Nme and Ace‐Gly‐Nme di‐peptides calculated using MP2/cc‐pVTZ//HF/6‐31G** quantum mechanical methods. All other parameters were taken from the existing AMBER data base. The major departure from previous force fields is that all quantum mechanical calculations were done in the condensed phase with continuum solvent models and an effective dielectric constant of ε = 4. We anticipate that this force field parameter set will address certain critical short comings of previous force fields in condensed‐phase simulations of proteins. Initial tests on peptides demonstrated a high‐degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace‐Gly‐Nme and Ace‐Ala‐Nme di‐peptides. Some highlights of our results include (1) well‐preserved balance between the extended and helical region distributions, and (2) favorable type‐II poly‐proline helical region in agreement with recent experiments. Backward compatibility between the new and Cornell et al. charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand‐binding calculations. Test simulations on a large set of proteins are also discussed. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1999–2012, 2003

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Metadata

Authors
Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., Caldwell, J., Wang, J., & Kollman, P.
Venue
Journal of Computational Chemistry
Publisher
Wiley
Published
2003-09-25
Volume
24
Issue
16
Pages
1999-2012
ISSN
  • 0192-8651 (ISSN-L)
  • 1096-987X
DOI
10.1002/jcc.10349
OpenAlex
W2069123478
Cited by
4,441
References
2
FWCI
9.01
Type
journal article
Language
en
Open access
closed

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