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Improved Treatment of the Protein Backbone in Empirical Force Fields
Abstract
Empirical force field-based calculations of proteins, including protein-folding studies, have improved our understanding of the relationship of their structure to their biological function. However, limitations in the accuracy of empirical force fields in the treatment of the peptide backbone exist. Presented is a grid correction approach to improve the treatment of the peptide backbone phi/psi conformational energies. Inclusion of this correction with the CHARMM22 all-atom protein force field is shown to lead to significant improvement in the treatment of the conformational energies of both the peptide model compound, the alanine dipeptide, and of proteins in their crystal environment. The developed approach is suggested to lead to significant improvements in the accuracy of empirical force fields to treat peptides and proteins.
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Cited by
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Entropic Stabilization of Proteins by TMAO
Cho, S. S., Reddy, G., Straub, J. E., & Thirumalai, D. (2011) · The Journal of Physical Chemistry B · doi:10.1021/jp207289b · Cited by 198
Modeling the structure of the StART domains of MLN64 and StAR proteins in complex with cholesterol
Murcia, M., Faráldo-Gómez, J. D., Maxfield, F. R., & Roux, B. (2006) · Journal of Lipid Research · doi:10.1194/jlr.m600232-jlr200 · Cited by 111
Biomolecular simulation and modelling: status, progress and prospects
van der Kamp, M. W., Shaw, K. E., Woods, C. J., & Mulholland, A. J. (2008) · Journal of The Royal Society Interface · doi:10.1098/rsif.2008.0105.focus · Cited by 90
Structural Features of the αβTCR Mechanotransduction Apparatus That Promote pMHC Discrimination
Brazin, K. N., Mallis, R. J., Das, D. K., Feng, Y., Hwang, W., Wang, J.-H., Wagner, G., Lang, M. J., & Reinherz, E. L. (2015) · Frontiers in Immunology · doi:10.3389/fimmu.2015.00441 · Cited by 70
Metadata
- Authors
- MacKerell, A. D., Feig, M., & Brooks, C. L.
- Venue
- Journal of the American Chemical Society
- Publisher
- American Chemical Society (ACS)
- Published
- 2003-12-30
- Volume
- 126
- Issue
- 3
- Pages
- 698-699
- ISSN
- 0002-7863 (ISSN-L)
- 1520-5126
- OpenAlex
- W1974030600
- Cited by
- 984
- References
- 0
- FWCI
- 4.29
- Type
- journal article
- Language
- en
- Open access
- closed
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
