Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles.
Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles.
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DOI：
10.1007/s12551-022-01015-8
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发表时间：
2022-12
影响因子：
--
通讯作者：
Kasahara, Kota
中科院分区：
文献类型：
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作者：
Fukunishi, Yoshifumi;Higo, Junichi;Kasahara, Kota
配体-受体复合物结构的预测在基础科学和药物发现等工业领域都具有重要意义。我们报告了各种计算分子对接方法：基本的计算机（虚拟）筛选，系综对接，增强采样（广义系综）的方法，和其他方法，以提高复杂结构的准确性。我们不仅解释了这些方法的优点，但它们的应用范围，并讨论了一些相互作用项，这是不考虑在硅片的方法。当人们专注于获得天然复合物结构（最稳定的复合物）时，计算机筛选和集成对接是有用的。广义系综方法提供了一个自由能景观，它显示了构象空间中最稳定的复杂结构和半稳定结构的分布。此外，隔离这些稳定的结构的障碍。研究者应根据研究目的和所研究的分子系统的复杂性选择其中一种方法。
Prediction of ligand-receptor complex structure is important in both the basic science and the industry such as drug discovery. We report various computation molecular docking methods: fundamental in silico (virtual) screening, ensemble docking, enhanced sampling (generalized ensemble) methods, and other methods to improve the accuracy of the complex structure. We explain not only the merits of these methods but also their limits of application and discuss some interaction terms which are not considered in the in silico methods. In silico screening and ensemble docking are useful when one focuses on obtaining the native complex structure (the most thermodynamically stable complex). Generalized ensemble method provides a free-energy landscape, which shows the distribution of the most stable complex structure and semi-stable ones in a conformational space. Also, barriers separating those stable structures are identified. A researcher should select one of the methods according to the research aim and depending on complexity of the molecular system to be studied.
DOI：
10.3390/ph5101064
发表时间：
2012-09-28
期刊：
Pharmaceuticals (Basel, Switzerland)
影响因子：
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作者：
Fukunishi Y;Nakamura H
通讯作者：
Nakamura H