Linear Interaction Energy: Method and Applications in Drug Design
Linear Interaction Energy: Method and Applications in Drug Design
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DOI：
10.1007/978-1-61779-465-0_20
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发表时间：
2012-01-01
期刊：
影响因子：
--
通讯作者：
Aqvist, Johan
中科院分区：
文献类型：
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作者：
Guitierrez-de-Teran, Hugo;Aqvist, Johan
存在广泛的计算方法来估计配体蛋白质的结合亲和力。在本章中，我们将提供一个用于结合自由能计算的线性相互作用能（LIE）方法的指南，重点是药物设计问题。该方法与所考虑的配体和配合物的相关构象的分子动力学（MD）采样相结合实现。MD取样的详细程序之后是关键注意事项，以便正确分析这种取样并获得配体结合亲和力的足够准确的估计。
A broad range of computational methods exist for the estimation of ligand protein binding affinities. In this chapter we will provide a guide to the linear interaction energy (LIE) method for binding free energy calculations, focusing on the drug design problem. The method is implemented in combination with molecular dynamics (MD) sampling of relevant conformations of the ligands and complexes under consideration. The detailed procedure for MD sampling is followed by key notes in order to properly analyze such sampling and obtain sufficiently accurate estimations of ligand-binding affinities.