Replica-Exchange and Standard State Binding Free Energies with Grand Canonical Monte Carlo
Replica-Exchange and Standard State Binding Free Energies with Grand Canonical Monte Carlo
复制标题
副本交换和标准状态与大正则蒙特卡罗结合自由能
DOI：
--
复制
发表时间：
2017
影响因子：
5.5
通讯作者：
J. Essex
中科院分区：
文献类型：
--
作者：
Gregory A. Ross;Hannah E. Bruce Macdonald;Christopher Cave;Ana I Cabedo Martinez;J. Essex
巨正则蒙特卡罗（GCMC）的能力，创建和湮灭分子在一个给定的区域，大大有助于识别水网站和水结合自由能的蛋白质腔。然而，不应用有偏移动的接受率可能很低，导致观测到的水占有率变化很大。在这里，我们表明，复制交换的化学势显着降低了GCMC数据的方差。当模拟由不同化学势的运行组成时，这种改进在计算费用上的增加可以忽略不计。复制交换GCMC也被发现大大提高精度的水结合自由能计算与巨正则积分，这使我们能够解决一个缺失的标准状态校正。
The ability of grand canonical Monte Carlo (GCMC) to create and annihilate molecules in a given region greatly aids the identification of water sites and water binding free energies in protein cavities. However, acceptance rates without the application of biased moves can be low, resulting in large variations in the observed water occupancies. Here, we show that replica-exchange of the chemical potential significantly reduces the variance of the GCMC data. This improvement comes at a negligible increase in computational expense when simulations comprise of runs at different chemical potentials. Replica-exchange GCMC is also found to substantially increase the precision of water binding free energies as calculated with grand canonical integration, which has allowed us to address a missing standard state correction.
登录
查看更多内容
影响因子：
2.9
作者：
Stone, John E.;Hardy, David J.;Ufimtsev, Ivan S.;Schulten, Klaus
通讯作者：
Schulten, Klaus
影响因子：
7.3
作者：
Nasief, Nader N.;Tan, Hongwei;Kong, Jing;Hangauert, David
通讯作者：
Hangauert, David
影响因子：
3.5
作者：
P. Mikulskis;D. Cioloboc;Milica Andrejic;Sakshi Khare;Joakim Brorsson;S. Genheden;R. Mata;Pär Söderhjelm;U. Ryde
通讯作者：
P. Mikulskis;D. Cioloboc;Milica Andrejic;Sakshi Khare;Joakim Brorsson;S. Genheden;R. Mata;Pär Söderhjelm;U. Ryde
影响因子：
4.4
作者：
Shirts, Michael R.;Chodera, John D.
通讯作者：
Chodera, John D.
影响因子：
5.5
作者：
Maier JA;Martinez C;Kasavajhala K;Wickstrom L;Hauser KE;Simmerling C
通讯作者：
Simmerling C