Fedorov Dmitri G, Kitaura Kazuo
Research Institute for Computational Sciences (RICS), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki, Japan 305-8568.
J Phys Chem A. 2007 Aug 2;111(30):6904-14. doi: 10.1021/jp0716740. Epub 2007 May 19.
Following the brief review of the modern fragment-based methods and other approaches to perform quantum-mechanical calculations of large systems, the theoretical development of the fragment molecular orbital method (FMO) is covered in detail, with the emphasis on the physical properties, which can be computed with FMO. The FMO-based polarizable continuum model (PCM) for treating the solvent effects in large systems and the pair interaction energy decomposition analysis (PIEDA) are described in some detail, and a range of applications of FMO to biological studies is introduced. The factors determining the relative stability of polypeptide conformers (alpha-helix, beta-turn, and extended form) are elucidated using FMO/PCM and PIEDA, and the interactions in the Trp-cage miniprotein construct (PDB: 1L2Y) are analyzed using PIEDA.
在简要回顾了用于对大型系统进行量子力学计算的现代基于片段的方法和其他方法之后，详细介绍了片段分子轨道方法（FMO）的理论发展，重点是可以用FMO计算的物理性质。详细描述了用于处理大型系统中溶剂效应的基于FMO的极化连续介质模型（PCM）和对相互作用能分解分析（PIEDA），并介绍了FMO在生物学研究中的一系列应用。使用FMO/PCM和PIEDA阐明了决定多肽构象异构体（α-螺旋、β-转角和伸展形式）相对稳定性的因素，并使用PIEDA分析了色氨酸笼状微蛋白构建体（PDB：1L2Y）中的相互作用。
