Subsystem Analysis for the Fragment Molecular Orbital Method and Its Application to Protein–Ligand Binding in Solution

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• 作者：Dmitri G. Fedorov ; Kazuo Kitaura
• 刊名：Journal of Physical Chemistry A
• 出版年：2016
• 出版时间：April 14, 2016
• 年：2016
• 卷：120
• 期：14
• 页码：2218-2231
• 全文大小：844K
• 年卷期：0
• ISSN：1520-5215

文摘

A subsystem analysis is derived incorporating interfragment interactions into the fragment properties, such as energies or charges. The relative stabilities of three alanine isomers, the α-helix, the β-turn, and the extended form are studied and the differences in fragment properties are elucidated. The analysis is further elaborated for studies of binding energies. The binding of the Trp-cage protein (PDB: 1L2Y) to two ligands is studied in detail. Binding energies defined for each fragment can be used as a convenient descriptor for analyzing contributions to binding in solution.