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Yuto Komeiji
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Fragment molecular orbital method: analytical energy gradients
K Kitaura, SI Sugiki, T Nakano, Y Komeiji, M Uebayasi
Chemical physics letters 336 (1-2), 163-170, 2001
2472001
Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems
S Tanaka, Y Mochizuki, Y Komeiji, Y Okiyama, K Fukuzawa
Physical Chemistry Chemical Physics 16 (22), 10310-10344, 2014
2352014
Fragment molecular orbital method: application to molecular dynamics simulation,‘ab initio FMO-MD’
Y Komeiji, T Nakano, K Fukuzawa, Y Ueno, Y Inadomi, T Nemoto, ...
Chemical physics letters 372 (3-4), 342-347, 2003
1252003
Intra‐ and intermolecular interactions between cyclic‐AMP receptor protein and DNA: Ab initio fragment molecular orbital study
K Fukuzawa, Y Komeiji, Y Mochizuki, A Kato, T Nakano, S Tanaka
Journal of computational chemistry 27 (8), 948-960, 2006
1102006
Fast and accurate molecular dynamics simulation of a protein using a special‐purpose computer
Y Komeiji, M Uebayasi, R Takata, A Shimizu, K Itsukashi, M Taiji
Journal of Computational Chemistry 18 (12), 1546-1563, 1997
1101997
How does an SN2 reaction take place in solution? Full ab initio MD simulations for the hydrolysis of the methyl diazonium ion
M Sato, H Yamataka, Y Komeiji, Y Mochizuki, T Ishikawa, T Nakano
Journal of the American Chemical Society 130 (8), 2396-2397, 2008
792008
Molecular dynamics simulations revealed Ca2+-dependent conformational change of calmodulin
Y Komeiji, Y Ueno, M Uebayasi
FEBS letters 521 (1-3), 133-139, 2002
762002
Computational observation of an ion permeation through a channel protein
A Suenaga, Y Komeiji, M Uebayasi, T Meguro, M Saito, I Yamato
Bioscience reports 18 (1), 39-48, 1998
761998
Change in a protein's electronic structure induced by an explicit solvent: An ab initio fragment molecular orbital study of ubiquitin
Y Komeiji, T Ishida, DG Fedorov, K Kitaura
Journal of Computational Chemistry 28 (10), 1750-1762, 2007
742007
Fragment molecular orbital based interaction analyses on COVID-19 main protease− inhibitor N3 complex (PDB ID: 6LU7)
R Hatada, K Okuwaki, Y Mochizuki, Y Handa, K Fukuzawa, Y Komeiji, ...
Journal of chemical information and modeling 60 (7), 3593-3602, 2020
682020
Fragment molecular orbital-based molecular dynamics (FMO-MD), a quantum simulation tool for large molecular systems
Y Komeiji, Y Mochizuki, T Nakano, DG Fedorov
Journal of Molecular Structure: THEOCHEM 898 (1-3), 2-7, 2009
652009
A fully quantum mechanical simulation study on the lowest n–π∗ state of hydrated formaldehyde
Y Mochizuki, Y Komeiji, T Ishikawa, T Nakano, H Yamataka
Chemical physics letters 437 (1-3), 66-72, 2007
652007
Fragment Molecular Orbital method‐based Molecular Dynamics (FMO‐MD) as a simulator for chemical reactions in explicit solvation
Y Komeiji, T Ishikawa, Y Mochizuki, H Yamataka, T Nakano
Journal of computational chemistry 30 (1), 40-50, 2009
622009
Three-body expansion and generalized dynamic fragmentation improve the fragment molecular orbital-based molecular dynamics (FMO-MD)
Y Komeiji, Y Mochizuki, T Nakano
Chemical Physics Letters 484 (4-6), 380-386, 2010
602010
A molecular dynamics study of solvent behavior around a protein
Y Komeiji, M Uebayasi, J Someya, I Yamato
Proteins: Structure, Function, and Bioinformatics 16 (3), 268-277, 1993
601993
PEACH 4 with ABINIT-MP: a general platform for classical and quantum simulations of biological molecules.
Y Komeiji, Y Inadomi, T Nakano
Computational Biology and Chemistry 28 (2), 155-161, 2004
572004
Fragment molecular orbital calculations on large scale systems containing heavy metal atom
T Ishikawa, Y Mochizuki, T Nakano, S Amari, H Mori, H Honda, T Fujita, ...
Chemical physics letters 427 (1-3), 159-165, 2006
552006
Fragment molecular orbital-based molecular dynamics (FMO-MD) method with MP2 gradient
Y Mochizuki, T Nakano, Y Komeiji, K Yamashita, Y Okiyama, ...
Chemical Physics Letters 504 (1-3), 95-99, 2011
452011
Visualization analysis of inter-fragment interaction energies of CRP–cAMP–DNA complex based on the fragment molecular orbital method
I Kurisaki, K Fukuzawa, Y Komeiji, Y Mochizuki, T Nakano, J Imada, ...
Biophysical chemistry 130 (1-2), 1-9, 2007
452007
Ab initio fragment molecular orbital (FMO) method applied to analysis of the ligand–protein interaction in a pheromone-binding protein
T Nemoto, DG Fedorov, M Uebayasi, K Kanazawa, K Kitaura, Y Komeiji
Computational Biology and Chemistry 29 (6), 434-439, 2005
432005
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