Yuto Komeiji

发表

Fast and accurate molecular dynamics simulation of a protein using a special-purpose computer

Makoto Taiji, Yuto Komeiji, Masami Uebayasi, 1997, J. Comput. Chem..

Intra‐ and intermolecular interactions between cyclic‐AMP receptor protein and DNA: Ab initio fragment molecular orbital study

Shigenori Tanaka, Yuto Komeiji, Tatsuya Nakano, 2006, J. Comput. Chem..

Fragment Molecular Orbital method‐based Molecular Dynamics (FMO‐MD) as a simulator for chemical reactions in explicit solvation

Takeshi Ishikawa, Yuto Komeiji, Tatsuya Nakano, 2009, J. Comput. Chem..

Intra‐ and intermolecular interactions between cyclic‐AMP receptor protein and DNA: Ab initio fragment molecular orbital study

Shigenori Tanaka, Yuto Komeiji, Tatsuya Nakano, 2007, J. Comput. Chem..

Water-mediated interactions in the CRP-cAMP-DNA complex: Does water mediate sequence-specific binding at the DNA primary-kink site?

Shigenori Tanaka, Yuto Komeiji, Kaori Fukuzawa, 2008, Comput. Biol. Chem..

Parallel molecular dynamics simulation of a protein

Makoto Haraguchi, Umpei Nagashima, Yuto Komeiji, 2001, Parallel Comput..

Peach-Grape system - a high performance simulator for biomolecules

Yuto Komeiji, Masami Uebayasi, 2002 .

Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease − Inhibitor N3 Complex (PDB ID: 6LU7)

Shigenori Tanaka, Yuto Komeiji, Kaori Fukuzawa, 2020, J. Chem. Inf. Model..

Ab initio fragment molecular orbital (FMO) method applied to analysis of the ligand-protein interaction in a pheromone-binding protein

Yuto Komeiji, Masami Uebayasi, Kazuo Kitaura, 2005, Comput. Biol. Chem..

Change in a protein's electronic structure induced by an explicit solvent: An ab initio fragment molecular orbital study of ubiquitin

Yuto Komeiji, Kazuo Kitaura, Dmitri G. Fedorov, 2007, J. Comput. Chem..

The ABINIT-MP Program

Hirotoshi Mori, Yoshinobu Akinaga, Yuto Komeiji, 2021 .

Fragment molecular orbital-based molecular dynamics (FMO-MD) method with MP2 gradient

Yuto Komeiji, Yuji Mochizuki, Hiroshi Yamataka, 2011 .

Fragment molecular orbital-based molecular dynamics (FMO-MD), a quantum simulation tool for large molecular systems

Yuto Komeiji, Yuji Mochizuki, Dmitri G. Fedorov, 2009 .

Fast and accurate molecular dynamics simulation of a protein using a special‐purpose computer

Makoto Taiji, Yuto Komeiji, Masami Uebayasi, 1997 .

Visualization analysis of inter-fragment interaction energies of CRP-cAMP-DNA complex based on the fragment molecular orbital method.

Yuto Komeiji, Kaori Fukuzawa, Yuji Mochizuki, 2007, Biophysical chemistry.

Fragment molecular orbital method: application to molecular dynamics simulation, ‘ab initio FMO-MD’

Yuichi Inadomi, Yutaka Ueno, Yuto Komeiji, 2003 .

Application of TensorFlow to recognition of visualized results of fragment molecular orbital (FMO) calculations

Yuto Komeiji, Yuji Mochizuki, Koji Okuwaki, 2018, 1801.07972.

Three-body expansion and generalized dynamic fragmentation improve the fragment molecular orbital-based molecular dynamics (FMO-MD)☆

Yuto Komeiji, Yuji Mochizuki, Tatsuya Nakano, 2010 .

Fragment molecular orbital method: analytical energy gradients

Yuto Komeiji, Masami Uebayasi, Kazuo Kitaura, 2001 .

Molecular dynamics simulations revealed Ca2+‐dependent conformational change of Calmodulin

Yutaka Ueno, Yuto Komeiji, Masami Uebayasi, 2002, FEBS letters.

Implementation of the blue moon ensemble method

Yuto Komeiji, 2007 .

Yuto Komeiji, Kaori Fukuzawa, Yuji Mochizuki, 2014, Physical chemistry chemical physics : PCCP.

PEACH 4 with ABINIT-MP: a general platform for classical and quantum simulations of biological molecules.

Yuichi Inadomi, Yuto Komeiji, Tatsuya Nakano, 2004, Computational biology and chemistry.

Flexibility of a loop in a pheromone binding protein from Bombyx mori: a molecular dynamics simulation

Yuto Komeiji, Masami Uebayashi, Tadashi Nemoto, 2002 .

Molecular dynamics simulation of trp-repressor/operator complex: analysis of hydrogen bond patterns of protein–DNA interaction

Ichiro Yamato, Yuto Komeiji, Masami Uebayasi, 2000 .

Molecular Dynamics Simulation of the Hin-Recombinase—DNA Complex

Yuto Komeiji, Masami Uebayasi, Y. Komeiji, 1999 .

A fully quantum mechanical simulation study on the lowest n-π* state of hydrated formaldehyde

Takeshi Ishikawa, Yuto Komeiji, Yuji Mochizuki, 2007 .

FMO-MD simulations on the hydration of formaldehyde in water solution with constraint dynamics.

Yuto Komeiji, Yuji Mochizuki, Hiroshi Yamataka, 2012, Chemistry.

How does an S(N)2 reaction take place in solution? Full ab initio MD simulations for the hydrolysis of the methyl diazonium ion.

Takeshi Ishikawa, Yuto Komeiji, Yuji Mochizuki, 2008, Journal of the American Chemical Society.

Fragment molecular orbital calculations on large scale systems containing heavy metal atom

Takeshi Ishikawa, Hiroaki Tokiwa, Hirotoshi Mori, 2006 .