What makes it difficult to refine protein models further via molecular dynamics simulations?
What makes it difficult to refine protein models further via molecular dynamics simulations?
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作者：
Heo L;Feig M
蛋白质结构细化仍然是一个具有挑战性但又重要的问题，因为它有可能使基于模板的精确模型达到接近原始的分辨率。基于分子动力学模拟的细化是一种非常有前途的方法，这里描述了 Feig 小组在 CASP12 期间基于 MD 的细化的表现。在 CASP12 期间，采样扩展到微秒级，应用了改进的力场，并测试了新的协议变化。发现前几轮 CASP 的进展有限，这是根据初始模型的质量以及对采样数量和细化协议变化的依赖性进行分析的。由于当前基于 MD 的细化协议似乎已达到稳定水平，因此提出了详细的分析，以便为更广泛的结构细化的主要挑战提供新的见解，特别关注有约束和无约束的采样。
Protein structure refinement remains a challenging yet important problem as it has the potential to bring already accurate template-based models to near-native resolution. Refinement based on molecular dynamics simulations has been a highly promising approach and the performance of MD-based refinement in the Feig group during CASP12 is described here. During CASP12, sampling was extended well into the microsecond scale, an improved force field was applied, and new protocol variations were tested. Progress over previous rounds of CASP was found to be limited which is analyzed in terms of the quality of the initial models and dependency on the amount of sampling and refinement protocol variations. As current MD-based refinement protocols appear to be reaching a plateau, detailed analysis is presented to provide new insight into the major challenges towards more extensive structure refinement, focusing in particular on sampling with and without restraints.
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影响因子：
2.9
作者：
Mirjalili, Vahid;Noyes, Keenan;Feig, Michael
通讯作者：
Feig, Michael
通过分子动力学系综的结构选择和平均来细化蛋白质结构。
影响因子：
5.5
作者：
Mirjalili, Vahid;Feig, Michael
通讯作者：
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影响因子：
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作者：
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通讯作者：
Kühlbrandt W
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作者：
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通讯作者：
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影响因子：
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作者：
JORGENSEN, WL;CHANDRASEKHAR, J;KLEIN, ML
通讯作者：
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