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通过结合不同的MD协议和力场来进行循环的强有力的 conformational空间探索

Samuel Murail¹, Jaysen Sawmynaden², Akli Zemirli¹

¹Université Paris Cité, CNRS UMR 8251, INSERM ERL U1133, Unité de Biologie Fonctionnelle et Adaptative, BFA, F-75013 Paris, France.

Journal of chemical theory and computation

|September 26, 2025

概括

探索循环形状需要多个模拟协议. 将四个隐性溶剂模拟与Amber96和Amber14力场相结合,可以有效地预测本地结构.

科学领域:

计算化学是一种计算化学.
生物物理学的生物物理.
药物发现药物发现

背景情况:

循环是重要的制药剂.
它们的形状景观是它们的功能关键.
对于九种设计的,已有实验性结构.

研究的目的:

探索九种周期性的构造格局.
评估不同力场和溶剂模型对模拟的影响.
确定最佳的模拟策略来预测原生结构.

主要方法:

复制品交换分子动力学 (REMD) 和模拟炼 (ST) 模拟.
测试Amber96,Amber14,RSFF2C和Charmm36m的力场. 测试Amber96,Amber14,RSFF2C和Charmm36m的力场. 测试Amber96,Amber14,RSFF2C和Charmm36m的力场. 测试Amber96,Amber14,RSFF2C和Charmm36m的力场. 测试Amber96,Amber14,RSFF2C和Charmm36m的力场. 测试Amber96,Amber14,RSFF2C和Charmm36m的力场. 测试Amber96,Amber14的力场. 测试Amber36m的力场.
使用隐式和显式溶剂模型.

主要成果:

协议的可变性超过了运行到运行的可变性,突出显示了对多个协议的需求.
自由能源地图显示了剩余的灵活性,一些低能量状态偏离了原生结构.
四个隐性溶剂REMD/ST模拟与Amber96/Amber14力场的组合可稳定地预测原生结构.

结论:

多个模拟协议对于可靠的结构分析至关重要.
隐式溶剂模拟为循环形状研究提供了一个计算效率高的策略.
一个实用的指导方针建议使用四个隐式溶剂模拟与混合力场强大的本地结构预测的混合力场.

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