Subsystem Analysis for the Fragment Molecular Orbital Method and Its Application to Protein-Ligand Binding in Solution
Subsystem Analysis for the Fragment Molecular Orbital Method and Its Application to Protein-Ligand Binding in Solution
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DOI：
10.1021/acs.jpca.6b00163
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发表时间：
2016-04-14
影响因子：
2.9
通讯作者：
Kitaura, Kazuo
中科院分区：
文献类型：
--
作者：
Fedorov, Dmitri G.;Kitaura, Kazuo
将碎片间相互作用合并到碎片属性（例如能量或电荷）中而得出子系统分析。研究了三种丙氨酸异构体（α-螺旋、β-转角和延伸形式）的相对稳定性，并阐明了片段特性的差异。该分析进一步用于结合能的研究。详细研究了色氨酸笼蛋白 (PDB: 1L2Y) 与两个配体的结合。为每个片段定义的结合能可用作分析对溶液中结合的贡献的方便描述符。
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 alpha-helix, the beta-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.