List of works - Koji Ogata

A Basic Quantum Chemical Review on the Activation of CO2

scientific article published in January 2015

A Monte Carlo sampling method of amino acid sequences adaptable to given main-chain atoms in the proteins.

scientific article

A study on an unusual SN2 mechanism in the methylation of benzyne through nickel-complexation.

scientific article published on 28 September 2017

Activation of CO2 by ionic liquid EMIM-BF4 in the electrochemical system: a theoretical study

scientific article published on 24 August 2015

Activators of cylindrical proteases as antimicrobials: identification and development of small molecule activators of ClpP protease

scientific article published in September 2011

All-atom molecular dynamics simulation of photosystem II embedded in thylakoid membrane

scientific article published on 14 October 2013

Amino acid similarity matrix for homology modeling derived from structural alignment and optimized by the Monte Carlo method

scientific article published in August 1998

An automatic homology modeling method consisting of database searches and simulated annealing

article

An electrostatic switch displaces phosphatidylinositol phosphate kinases from the membrane during phagocytosis

scientific article

An electrostatic switch displaces phosphatidylinositol phosphate kinases from the membrane during phagocytosis

Automatic sequence design of major histocompatibility complex class I binding peptides impairing CD8+ T cell recognition

scientific article

Binding free-energy calculation is a powerful tool for drug optimization: calculation and measurement of binding free energy for 7-azaindole derivatives to glycogen synthase kinase-3β

scientific article published on 11 June 2014

CRYBA4, a novel human cataract gene, is also involved in microphthalmia

scientific article

Conserved water molecules in MHC class-I molecules and their putative structural and functional roles

scientific article

Diastereomeric resolution directed towards chirality determination focussing on gas-phase energetics of coordinated sodium dissociation

scientific article

Direct binding targets of the stringent response alarmone (p)ppGpp

scientific article

Effect of Atomic Charges on Octanol-Water Partition Coefficient Using Alchemical Free Energy Calculation

scientific article published on 15 February 2018

Improvement of Parameters of the AMBER Potential Force Field for Phospholipids for Description of Thermal Phase Transitions

scientific article published on 10 July 2015

Investigation of a Pathway for Water Delivery in Photosystem II Protein by Molecular Dynamics Simulation

scientific article published on 18 July 2019

Lead generation and optimization based on protein-ligand complementarity.

scientific article published on 17 June 2010

Mechanistic basis of pre–T cell receptor–mediated autonomous signaling critical for thymocyte development

article

Mincle is an ITAM-coupled activating receptor that senses damaged cells

scientific journal article

Modeling the three-dimensional structure of H+-ATPase of Neurospora crassa

scientific article

Mutations in chaperonin-like BBS genes are a major contributor to disease development in a multiethnic Bardet-Biedl syndrome patient population

scientific article published on 14 May 2010

New insights into highly efficient reduction of CO2 to formic acid by using zinc under mild hydrothermal conditions: a joint experimental and theoretical study.

scientific article published in October 2014

Photochromism of 1,2-Bis(2-thienyl)perfluorocyclopentene Derivatives: Substituent Effect on the Reactive Carbon Atoms

scientific article published on 01 November 2012

Prediction of protein side-chain conformations by principal component analysis for fixed main-chain atoms.

scientific article published on April 1997

Quality Assessment of Predicted Protein Models Using Energies Calculated by the Fragment Molecular Orbital Method.

scientific article

Structural changes in the S3 state of the oxygen evolving complex in photosystem II.

scientific article published on 19 March 2016

The role played by environmental residues on sidechain torsional angles within homologous families of proteins: a new method of sidechain modeling

scientific article published in June 1998

Theoretical Study on the Role of Ca2+ at the S2 State in Photosystem II

scientific article published on 24 November 2014

Theoretical study on carbon-carbon short contact of ∼2.3 Å: intermediate state between nonbonding and σ-covalent bonding.

scientific article

Understanding Thermal Phases in Atomic Detail by All-Atom Molecular-Dynamics Simulation of a Phospholipid Bilayer

article

Unrestricted Hartree-Fock based on the fragment molecular orbital method: Energy and its analytic gradient

scientific article published on 01 July 2012

List of works by Koji Ogata

A Basic Quantum Chemical Review on the Activation of CO2

A Monte Carlo sampling method of amino acid sequences adaptable to given main-chain atoms in the proteins.

A study on an unusual SN2 mechanism in the methylation of benzyne through nickel-complexation.

Activation of CO2 by ionic liquid EMIM-BF4 in the electrochemical system: a theoretical study

Activators of cylindrical proteases as antimicrobials: identification and development of small molecule activators of ClpP protease

All-atom molecular dynamics simulation of photosystem II embedded in thylakoid membrane

Amino acid similarity matrix for homology modeling derived from structural alignment and optimized by the Monte Carlo method

An automatic homology modeling method consisting of database searches and simulated annealing

An electrostatic switch displaces phosphatidylinositol phosphate kinases from the membrane during phagocytosis

An electrostatic switch displaces phosphatidylinositol phosphate kinases from the membrane during phagocytosis

Automatic sequence design of major histocompatibility complex class I binding peptides impairing CD8+ T cell recognition

Binding free-energy calculation is a powerful tool for drug optimization: calculation and measurement of binding free energy for 7-azaindole derivatives to glycogen synthase kinase-3β

CRYBA4, a novel human cataract gene, is also involved in microphthalmia

Conserved water molecules in MHC class-I molecules and their putative structural and functional roles

Diastereomeric resolution directed towards chirality determination focussing on gas-phase energetics of coordinated sodium dissociation

Direct binding targets of the stringent response alarmone (p)ppGpp

Effect of Atomic Charges on Octanol-Water Partition Coefficient Using Alchemical Free Energy Calculation

Improvement of Parameters of the AMBER Potential Force Field for Phospholipids for Description of Thermal Phase Transitions

Investigation of a Pathway for Water Delivery in Photosystem II Protein by Molecular Dynamics Simulation

Lead generation and optimization based on protein-ligand complementarity.

Mechanistic basis of pre–T cell receptor–mediated autonomous signaling critical for thymocyte development

Mincle is an ITAM-coupled activating receptor that senses damaged cells

Modeling the three-dimensional structure of H+-ATPase of Neurospora crassa

Mutations in chaperonin-like BBS genes are a major contributor to disease development in a multiethnic Bardet-Biedl syndrome patient population

New insights into highly efficient reduction of CO2 to formic acid by using zinc under mild hydrothermal conditions: a joint experimental and theoretical study.

Photochromism of 1,2-Bis(2-thienyl)perfluorocyclopentene Derivatives: Substituent Effect on the Reactive Carbon Atoms

Prediction of protein side-chain conformations by principal component analysis for fixed main-chain atoms.

Quality Assessment of Predicted Protein Models Using Energies Calculated by the Fragment Molecular Orbital Method.

Structural changes in the S3 state of the oxygen evolving complex in photosystem II.

The role played by environmental residues on sidechain torsional angles within homologous families of proteins: a new method of sidechain modeling

Theoretical Study on the Role of Ca2+ at the S2 State in Photosystem II

Theoretical study on carbon-carbon short contact of ∼2.3 Å: intermediate state between nonbonding and σ-covalent bonding.

Understanding Thermal Phases in Atomic Detail by All-Atom Molecular-Dynamics Simulation of a Phospholipid Bilayer

Unrestricted Hartree-Fock based on the fragment molecular orbital method: Energy and its analytic gradient