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Current Status of Protein Force Fields for Molecular Dynamics Simulations

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Molecular Modeling of Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1215))

Abstract

The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and AMOEBA polarizable force fields. Parametrization strategies developed specifically for the Drude force field are described and compared with the additive CHARMM36 force field. Results from molecular simulations of proteins and small peptides are summarized to illustrate the performance of the Drude and AMOEBA force fields.

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Acknowledgement

Financial support from the NIH (GM072558) and computational support from the University of Maryland Computer-Aided Drug Design Center, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number OCI-1053575, are acknowledged.

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Authors and Affiliations

  1. Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street HSFII, Baltimore, MD, 21201, USA

    Pedro E. M. Lopes & Alexander D. MacKerell Jr.

  2. Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, 716 Stevens Avenue, Portland, ME, 04103, USA

    Olgun Guvench

Authors
  1. Pedro E. M. Lopes
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  2. Olgun Guvench
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  3. Alexander D. MacKerell Jr.
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Corresponding author

Correspondence to Alexander D. MacKerell Jr. .

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Editors and Affiliations

  1. University of Hertfordshire, Hatfield, Hertfordshire, United Kingdom

    Andreas Kukol

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Lopes, P.E.M., Guvench, O., MacKerell, A.D. (2015). Current Status of Protein Force Fields for Molecular Dynamics Simulations. In: Kukol, A. (eds) Molecular Modeling of Proteins. Methods in Molecular Biology, vol 1215. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1465-4_3

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  • DOI: https://doi.org/10.1007/978-1-4939-1465-4_3

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-1464-7

  • Online ISBN: 978-1-4939-1465-4

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