Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States.
Department of Chemistry, University of Colombo, Colombo 00300, Sri Lanka.
J Chem Theory Comput. 2021 May 11;17(5):2964-2990. doi: 10.1021/acs.jctc.1c00075. Epub 2021 Apr 20.
A new classical nonpolarizable force field, KBFF20, for the simulation of peptides and proteins is presented. The force field relies heavily on the use of Kirkwood-Buff theory to provide a comparison of simulated and experimental Kirkwood-Buff integrals for solutes containing the functional groups common in proteins, thus ensuring intermolecular interactions that provide a good balance between the peptide-peptide, peptide-solvent, and solvent-solvent distributions observed in solution mixtures. In this way, it differs significantly from other biomolecular force fields. Further development and testing of the intermolecular potentials are presented here. Subsequently, rotational potentials for the ϕ/ψ and χ dihedral degrees of freedom are obtained by analysis of the Protein Data Bank, followed by small modifications to provide a reasonable balance between simulated and observed α and β percentages for small peptides. This, the first of two articles, describes in detail the philosophy and development behind KBFF20.
一种新的经典非极化力场 KBFF20 被提出用于模拟肽和蛋白质。该力场主要依赖于 Kirkwood-Buff 理论的应用，为含有蛋白质中常见官能团的溶质提供模拟和实验 Kirkwood-Buff 积分的比较，从而确保在溶液混合物中观察到的肽-肽、肽-溶剂和溶剂-溶剂相互作用之间的良好平衡。这样，它与其他生物分子力场有很大的不同。本文介绍了分子间相互作用势的进一步开发和测试。随后，通过对蛋白质数据库的分析得到了 ϕ/ψ 和 χ 二面角自由度的旋转势，然后进行了小的修改，以在模拟和观察到的小肽的α和β百分比之间提供合理的平衡。这是两篇文章中的第一篇，详细描述了 KBFF20 的背后的理念和发展。
