Improved treatment of the protein backbone in empirical force fields.

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TitleImproved treatment of the protein backbone in empirical force fields.
Publication TypeJournal Article
Year of Publication2004
AuthorsMackerell, AD, Feig, M, Brooks, CL
JournalJ Am Chem Soc
Volume126
Issue3
Pagination698-9
Date Published2004 Jan 28
ISSN0002-7863
KeywordsDipeptides, Glycine, Models, Chemical, Protein Conformation, Proteins, Static Electricity, Structure-Activity Relationship, Surface Properties, Thermodynamics
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.

DOI10.1021/ja036959e
Alternate JournalJ. Am. Chem. Soc.
PubMed ID14733527
Grant ListGM37554 / GM / NIGMS NIH HHS / United States
GM48807 / GM / NIGMS NIH HHS / United States
GM51505 / GM / NIGMS NIH HHS / United States
RR12255 / RR / NCRR NIH HHS / United States