Exploring chemistry with the fragment molecular orbital method

被引：293

作者：

Fedorov, Dmitri G. ^{[1
]}

Nagata, Takeshi ^{[1
,2
]}

Kitaura, Kazuo ^{[1
,2
]}

机构：

[1] Natl Inst Adv Ind Sci & Technol, NRI, Tsukuba, Ibaraki 3058568, Japan

[2] Kyoto Univ, Grad Sch Pharmaceut Sci, Sakyo Ku, Kyoto 6068501, Japan

来源：

PHYSICAL CHEMISTRY CHEMICAL PHYSICS | 2012年 / 14卷 / 21期

关键词：

POLARIZABLE CONTINUUM MODEL; PLESSET PERTURBATION-THEORY; DENSITY-FUNCTIONAL THEORY; INITIO MO CALCULATIONS; CH/PI HYDROGEN-BONDS; RETINOID-X-RECEPTOR; DYNAMICS FMO-MD; INFLUENZA VIRAL HEMAGGLUTININ; QUANTUM-CHEMICAL CALCULATION; A VIRUS HEMAGGLUTININ;

D O I：

10.1039/c2cp23784a

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

The fragment molecular orbital (FMO) method makes possible nearly linear scaling calculations of large molecular systems, such as water clusters, proteins and DNA. In particular, FMO has been widely used in biochemical applications involving protein-ligand binding and drug design. The method has been efficiently parallelized suitable for petascale computing. Many commonly used wave functions and solvent models have been interfaced with FMO. We review the historical background of FMO, and summarize its method development and applications.

引用

页码：7562 / 7577

页数：16

共 261 条

[1] VISCANA: Visualized cluster analysis of protein-ligand interaction based on the ab initio fragment molecular orbital method for virtual ligand screening
Amari, S
Aizawa, M
Zhang, JW
Fukuzawa, K
Mochizuki, Y
Iwasawa, Y
Nakata, K
Chuman, H
Nakano, T
[J]. JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2006, 46 (01) : 221 - 230
[2] [Anonymous], 2006, Modern Methods for Theoretical Physical Chemistry of Biopolymers, DOI [DOI 10.1016/B978-041152220-7/50066-6, DOI 10.1016/B978, 10.1016/B978]
[3] Highly accurate O(N) method for delocalized systems
Aoki, Yuriko
Loboda, Oleksandr
Liu, Kai
Makowski, Marcin A.
Gu, Feng Long
[J]. THEORETICAL CHEMISTRY ACCOUNTS, 2011, 130 (4-6) : 595 - 608
[4] Nuclear-Electronic Orbital Method within the Fragment Molecular Orbital Approach
Auer, Benjamin
Pak, Michael V.
Hammes-Schiffer, Sharon
[J]. JOURNAL OF PHYSICAL CHEMISTRY C, 2010, 114 (12) : 5582 - 5588
[5] Ab initio quality one-electron properties of large molecules: Development and testing of molecular tailoring approach
Babu, K
Gadre, SR
[J]. JOURNAL OF COMPUTATIONAL CHEMISTRY, 2003, 24 (04) : 484 - 495
[6] A new algorithm for molecular fragmentation in quantum chemical calculations
Bettens, Ryan P. A.
Lee, Adrian M.
[J]. JOURNAL OF PHYSICAL CHEMISTRY A, 2006, 110 (28) : 8777 - 8785
[7] MacMolPlt: A graphical user interface for GAMESS
Bode, BM
Gordon, MS
[J]. JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 1998, 16 (03) : 133 - +
[8] Structure and Dynamics of the 1-Hydroxyethyl-4-amino-1,2,4-triazolium Nitrate High-Energy Ionic Liquid System
Carlson, Philip J.
Bose, Sayantan
Armstrong, Daniel W.
Hawkins, Tommy
Gordon, Mark S.
Petrich, Jacob W.
[J]. JOURNAL OF PHYSICAL CHEMISTRY B, 2012, 116 (01) : 503 - 512
[9] Energy decomposition analyses for many-body interaction and applications to water complexes
Chen, W
Gordon, MS
[J]. JOURNAL OF PHYSICAL CHEMISTRY, 1996, 100 (34) : 14316 - 14328
[10] An efficient approach for ab initio energy calculation of biopolymers -: art. no. 184105
Chen, XH
Zhang, YK
Zhang, JZH
[J]. JOURNAL OF CHEMICAL PHYSICS, 2005, 122 (18)

← 1 2 3 4 5 6 7 8 9 10 →