Integration of Experimental Data and Use of Automated Fitting Methods in Developing Protein Force Fields.
Integration of Experimental Data and Use of Automated Fitting Methods in Developing Protein Force Fields.
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DOI：
10.1038/s42004-022-00653-z
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发表时间：
2022
影响因子：
5.9
通讯作者：
Lemkul JA
中科院分区：
文献类型：
--
作者：
Polêto MD;Lemkul JA
在过去的50年里，精确的蛋白质力场的发展一直是分子模拟的基石。在此期间，在使用实验目标数据和参数拟合程序方面吸取了许多经验教训。在这里，我们回顾了蛋白质力场发展的最新进展。我们讨论了最近出现的极化力场和电子极化的作用和领域，其中添加剂力场不足。自动拟合方法的使用和参数化过程中包含额外的实验解决方案数据进行了讨论，作为一种手段，突出可能的路线，以进一步提高力场的准确性。用于研究化学和生物物理过程的分子动力学模拟依赖于所用力场的准确性。在这里，作者回顾了在开发可加性和可极化力场方面的成功和关键困难领域，并讨论了实验数据的可用性，经验改进如何影响参数化，并强调了进一步提高力场准确性的可能途径。
The development of accurate protein force fields has been the cornerstone of molecular simulations for the past 50 years. During this period, many lessons have been learned regarding the use of experimental target data and parameter fitting procedures. Here, we review recent advances in protein force field development. We discuss the recent emergence of polarizable force fields and the role of electronic polarization and areas in which additive force fields fall short. The use of automated fitting methods and the inclusion of additional experimental solution data during parametrization is discussed as a means to highlight possible routes to improve the accuracy of force fields even further. Molecular dynamics simulations, used to study chemical and biophysical processes, rely on the accuracy of the employed force fields. Here, the authors review successes and key areas of difficulty in the development of additive and polarizable force fields, and discuss experimental data availability, how empirical refinement impacts parametrization, and highlight possible routes to further improve the accuracy of force fields.