Aldeghi Matteo, Bluck Joseph P, Biggin Philip C
Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, UK.
Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
Methods Mol Biol. 2018;1762:199-232. doi: 10.1007/978-1-4939-7756-7_11.
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.
许多热力学量可以从根据统计力学原理生成微观状态系综的计算机模拟中提取。在这些量中，有小分子与大分子（如蛋白质）结合的自由能。在这里，我们介绍一种通过分子动力学模拟来估计配体结合自由能的方法的入门概述。虽然我们专注于有机分子与蛋白质的结合，但该方法原则上可应用于任何一对分子。
