Improved treatment of the protein backbone in empirical force fields
Improved treatment of the protein backbone in empirical force fields
复制标题
DOI：
10.1021/ja036959e
复制
发表时间：
2004-01-28
影响因子：
15
通讯作者：
Brooks, CL
中科院分区：
文献类型：
--
作者：
MacKerell, AD;Feig, M;Brooks, CL
基于经验力场的蛋白质计算，包括蛋白质折叠研究，提高了我们对其结构与其生物功能关系的理解。然而，在处理肽骨架时，经验力场的准确性存在局限性。提出了一种网格校正方法来改善肽主链 φ/ψ 构象能的处理。将这种校正与 CHARMM22 全原子蛋白质力场结合起来，可以显着改善肽模型化合物、丙氨酸二肽及其晶体环境中蛋白质的构象能的处理。建议开发的方法可以显着提高处理肽和蛋白质的经验力场的准确性。
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 φ/ψ 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.