MacKerell Alexander D, Feig Michael, Brooks Charles L
Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, USA.
J Am Chem Soc. 2004 Jan 28;126(3):698-9. doi: 10.1021/ja036959e.
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.
基于经验力场的蛋白质计算，包括蛋白质折叠研究，增进了我们对其结构与生物学功能之间关系的理解。然而，经验力场在处理肽主链时存在精度限制。本文提出一种网格校正方法，以改进对肽主链φ/ψ构象能量的处理。结果表明，将此校正与CHARMM22全原子蛋白质力场相结合，能显著改善对肽模型化合物丙氨酸二肽以及晶体环境中蛋白质构象能量的处理。所开发的方法有望显著提高经验力场处理肽和蛋白质的精度。
