Absolute Alchemical Free Energy Calculations for Ligand Binding: A Beginner's Guide
Absolute Alchemical Free Energy Calculations for Ligand Binding: A Beginner's Guide
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DOI：
10.1007/978-1-4939-7756-7_11
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发表时间：
2018-01-01
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影响因子：
--
通讯作者：
Biggin, Philip C.
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文献类型：
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作者：
Aldeghi, Matteo;Bluck, Joseph P.;Biggin, Philip C.
许多热力学量可以从计算机模拟中提取，这些模拟根据统计力学原理生成微观状态的集合。在这些量中，有一个小分子与大分子（如蛋白质）结合的自由能。在这里，我们提出了一个协议，允许通过分子动力学模拟的配体结合自由能的估计的介绍性概述。虽然我们专注于有机分子与蛋白质的结合，但该方法原则上可转移到任何分子对。
Many thermodynamic quantities can be extracted from computer simulations that generate an ensemble of microstates according to the principles of statistical mechanics. Among these quantities is the free energy of binding of a small molecule to a macromolecule, such as a protein. Here, we present an introductory overview of a protocol that allows for the estimation of ligand binding free energies via molecular dynamics simulations. While we focus on the binding of organic molecules to proteins, the approach is in principle transferable to any pair of molecules.