Pairwise-additive and polarizable atomistic force fields for molecular dynamics simulations of proteins.

Progress in Molecular Biology and Translational Science
Justin A Lemkul

Abstract

Protein force fields have been undergoing continual development since the first complete parameter sets were introduced nearly four decades ago. The functional forms that underlie these models have many common elements for the treatment of bonded and nonbonded forces, which are reviewed here. The most widely used force fields to date use a fixed-charge convention in which electronic polarization effects are treated via a mean-field approximation during partial charge assignment. Despite success in modeling folded proteins over many years, the fixed-charge assumption has limitations that cannot necessarily be overcome within their potential energy equations. To overcome these limitations, several force fields have recently been derived that explicitly treat electronic polarization effects with straightforward extensions of the potential energy functions used by nonpolarizable force fields. Here, we review the history of the most popular nonpolarizable force fields (AMBER, CHARMM, OPLS, and GROMOS) as well as studies that have validated them and applied them to studies of protein folding and misfolding. Building upon these force fields are more recent polarizable interaction potentials, including fluctuating charge models, POSSIM...Continue Reading

Citations

Aug 7, 2020·Biochemical Society Transactions·Jane R Allison
Jan 13, 2021·Journal of Cheminformatics·Simon A BrayBjörn A Grüning

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