List of works - Yuto Komeiji

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

scientific article published on 10 November 2005

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

scientific article published on 01 July 2007

Change in conformation by DNA-peptide association: molecular dynamics of the Hin-recombinase-hixL complex

scientific article

Cm3+/Eu3+ induced structural, mechanistic and functional implications for calmodulin

scientific article published on 16 August 2019

Computational Observation of an Ion Permeation Through a Channel Protein ⬇️

scientific article published on February 1, 1998

Does amination of formaldehyde proceed through a zwitterionic intermediate in water? Fragment molecular orbital molecular dynamics simulations by using constraint dynamics

scientific article published on 01 June 2010

Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems

scientific article published on June 2014

FMO‐MD Simulations on the Hydration of Formaldehyde in Water Solution with Constraint Dynamics ⬇️

scientific article published on 02 July 2012

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

scientific article published on January 2009

Glycine 85 of the trp-repressor of E. coli is important in forming the hydrophobic tryptophan binding pocket: experimental and computational approaches

scientific article published on 01 October 1994

Helix propensity of Ala and Val: a free energy perturbation study

scientific article published on 01 August 1993

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

scientific article published on 02 February 2008

Hydration of ligands of influenza virus neuraminidase studied by the fragment molecular orbital method

scientific article published on 31 August 2016

Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: ab initio fragment molecular orbital study.

scientific article published in June 2006

Molecular dynamics simulation of trp-aporepressor in a solvent.

scientific article published in December 1991

Molecular dynamics simulations of trp apo- and holorepressors: domain structure and ligand-protein interaction

scientific article published on 01 November 1994

Molecular dynamics simulations revealed Ca(2+)-dependent conformational change of Calmodulin

scientific article published on 01 June 2002

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

scientific article

Threonine 81 of the trp repressor of Escherichia coli plays an auxiliary role in the formation of the corepressor binding pocket.

scientific article

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

scientific article published on 05 July 2007

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

scientific article published on 19 January 2008

List of works by Yuto Komeiji

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

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

Change in conformation by DNA-peptide association: molecular dynamics of the Hin-recombinase-hixL complex

Cm3+/Eu3+ induced structural, mechanistic and functional implications for calmodulin

Computational Observation of an Ion Permeation Through a Channel Protein ⬇️

Does amination of formaldehyde proceed through a zwitterionic intermediate in water? Fragment molecular orbital molecular dynamics simulations by using constraint dynamics

Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems

FMO‐MD Simulations on the Hydration of Formaldehyde in Water Solution with Constraint Dynamics ⬇️

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

Glycine 85 of the trp-repressor of E. coli is important in forming the hydrophobic tryptophan binding pocket: experimental and computational approaches

Helix propensity of Ala and Val: a free energy perturbation study

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

Hydration of ligands of influenza virus neuraminidase studied by the fragment molecular orbital method

Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: ab initio fragment molecular orbital study.

Molecular dynamics simulation of trp-aporepressor in a solvent.

Molecular dynamics simulations of trp apo- and holorepressors: domain structure and ligand-protein interaction

Molecular dynamics simulations revealed Ca(2+)-dependent conformational change of Calmodulin

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

Threonine 81 of the trp repressor of Escherichia coli plays an auxiliary role in the formation of the corepressor binding pocket.

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

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