Exploring chemistry with the fragment molecular orbital method

被引：295

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 50 条

[31] Fully analytic energy gradient in the fragment molecular orbital method
Nagata, Takeshi
Brorsen, Kurt
Fedorov, Dmitri G.
Kitaura, Kazuo
Gordon, Mark S.
JOURNAL OF CHEMICAL PHYSICS, 2011, 134 (12):
[32] Analytic second derivatives of the energy in the fragment molecular orbital method
Nakata, Hiroya
Nagata, Takeshi
Fedorov, Dmitri G.
Yokojima, Satoshi
Kitaura, Kazuo
Nakamura, Shinichiro
JOURNAL OF CHEMICAL PHYSICS, 2013, 138 (16):
[33] Fragment Molecular Orbital Method Adaptations for Heterogeneous Computing Platforms
Talamudupula, Sai Kiran
Sosonkina, Masha
Gaenko, Alexander
Schmidt, Michael W.
PROCEEDINGS OF THE INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE, ICCS 2012, 2012, 9 : 489 - 497
[34] Analyzing protein structure with the effective fragment molecular orbital method
Bertoni, Colleen
Pruitt, Spencer
Gordon, Mark
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2014, 248
[35] Open-Shell Formulation of the Fragment Molecular Orbital Method
Pruitt, Spencer R.
Fedorov, Dmitri G.
Kitaura, Kazuo
Gordon, Mark S.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2010, 6 (01) : 1 - 5
[36] The fragment molecular orbital method for geometry optimizations of polypeptides and proteins
Fedorov, Dmitri G.
Ishida, Toyokazu
Uebayasi, Masami
Kitaura, Kazuo
JOURNAL OF PHYSICAL CHEMISTRY A, 2007, 111 (14): : 2722 - 2732
[37] Analytic gradient for the adaptive frozen orbital bond detachment in the fragment molecular orbital method
Fedorov, Dmitri G.
Avramov, Pavel V.
Jensen, Jan H.
Kitaura, Kazuo
CHEMICAL PHYSICS LETTERS, 2009, 477 (1-3) : 169 - 175
[38] Molecular orbital analysis based on fragment molecular orbital scheme
Sekino, H
Sengoku, Y
Sugiki, S
Kurita, N
CHEMICAL PHYSICS LETTERS, 2003, 378 (5-6) : 589 - 597
[39] The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds
Steinmann, Casper
Fedorov, Dmitri G.
Jensen, Jan H.
PLOS ONE, 2012, 7 (07):
[40] Systematic Study of the Embedding Potential Description in the Fragment Molecular Orbital Method
Fedorov, Dmitri G.
Slipchenko, Lyudmila V.
Kitaura, Kazuo
JOURNAL OF PHYSICAL CHEMISTRY A, 2010, 114 (33): : 8742 - 8753

← 1 2 3 4 5 →