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Self-Avoiding Conformational Sampling Based on Histories of Past Conformational Searches
Journal of Chemical Information and Modeling ( IF 5.6 ) Pub Date : 2017-11-16 00:00:00 , DOI: 10.1021/acs.jcim.7b00573 Ryuhei Harada 1 , Yasuteru Shigeta 1
Journal of Chemical Information and Modeling ( IF 5.6 ) Pub Date : 2017-11-16 00:00:00 , DOI: 10.1021/acs.jcim.7b00573 Ryuhei Harada 1 , Yasuteru Shigeta 1
Affiliation
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Self-avoiding conformational sampling (SACS) is proposed as an enhanced conformational sampling method for proteins. In SACS, the following conformational resampling is repeated for a given protein: (1) identification of newly visited states in a subspace and (2) conformational resampling by restarting short-time molecular dynamics (MD) simulations from the newly visited states. To identify the newly visited states, a set of history-dependent histograms projected onto the subspace is used. One is constructed from the trajectories sampled at the current (ith) cycle, and the other is constructed from all of the trajectories accumulated up through the previous ((i – 1)th) cycle. By reference to the history-dependent histograms, the newly visited states appearing at the current (ith) cycle are defined as a difference set between them. By repeating the cycle of conformational resampling, SACS prevents the system from revisiting states that have already been visited for previous cycles, promoting structural transitions via resampling from the newly visited states. To verify the conformational sampling efficiency of SACS, the present method was applied to reveal underlying mechanisms of biologically important domain motions of maltodextrin binding protein in explicit water and successfully reproduced the open–closed transition with a reasonable (nanosecond-order) computational cost.
中文翻译：
基于过去构象搜索历史的自我避免构象抽样
自我规避构象采样（SACS）被提出作为一种增强的蛋白质构象采样方法。在SACS中，对给定的蛋白质重复以下构象重采样：（1）识别子空间中新近访问的状态，以及（2）通过从新近访问的状态重新启动短时分子动力学（MD）模拟，进行构象重采样。为了识别新访问的状态，使用了一组投影到子空间上的依赖历史的直方图。一个是从在当前（取样的轨迹构成我th）的周期，而另一个是从所有通过之前的（（积累起来的轨迹的构造我- 1）个）周期。通过参考与历史相关的直方图，新访问的状态出现在当前（i th）周期定义为它们之间的差异集。通过重复构象重采样的周期，SACS可以防止系统重新访问先前周期已访问的状态，从而通过从新访问的状态进行重采样来促进结构转换。为了验证SACS的构象采样效率，本方法被用于揭示麦芽糊精结合蛋白在显性水中的生物学上重要的域运动的潜在机制，并以合理的（纳秒级）计算成本成功地再现了开闭过渡。
更新日期：2017-11-16
中文翻译：
基于过去构象搜索历史的自我避免构象抽样
自我规避构象采样（SACS）被提出作为一种增强的蛋白质构象采样方法。在SACS中，对给定的蛋白质重复以下构象重采样：（1）识别子空间中新近访问的状态，以及（2）通过从新近访问的状态重新启动短时分子动力学（MD）模拟，进行构象重采样。为了识别新访问的状态，使用了一组投影到子空间上的依赖历史的直方图。一个是从在当前（取样的轨迹构成我th）的周期，而另一个是从所有通过之前的（（积累起来的轨迹的构造我- 1）个）周期。通过参考与历史相关的直方图，新访问的状态出现在当前（i th）周期定义为它们之间的差异集。通过重复构象重采样的周期，SACS可以防止系统重新访问先前周期已访问的状态，从而通过从新访问的状态进行重采样来促进结构转换。为了验证SACS的构象采样效率，本方法被用于揭示麦芽糊精结合蛋白在显性水中的生物学上重要的域运动的潜在机制，并以合理的（纳秒级）计算成本成功地再现了开闭过渡。
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