List of works - Yuko Okamoto

A pH-dependent variation in alpha-helix structure of the S-peptide of ribonuclease A studied by Monte Carlo simulated annealing

scientific article published in April 2002

A prediction of tertiary structures of peptide by the Monte Carlo simulated annealing method.

scientific article published on November 1989

Ab Initio prediction of protein-ligand binding structures by replica-exchange umbrella sampling simulations

scientific article published on 27 June 2011

Amino-acid-dependent main-chain torsion-energy terms for protein systems

Amyloid-beta(29-42) dimer formations studied by a multicanonical-multioverlap molecular dynamics simulation.

scientific article published on 14 February 2008

Analysis of helix-helix interactions of bacteriorhodopsin by replica-exchange simulations

scientific article published on February 2009

Beta-sheet folding of fragment (16-36) of bovine pancreatic trypsin inhibitor as predicted by Monte Carlo simulated annealing

scientific article published in September 1992

Characteristic temperatures of folding of a small peptide ⬇️

scientific article published on September 30, 1997

Classification and Prediction of Low-Energy Membrane Protein Helix Configurations by Replica-Exchange Monte Carlo Method

Classification of Low-Energy Conformations of Met-Enkephalin in the Gas Phase and in a Model Solvent Based on the Extended Scaled Particle Theory

article

Communication: Simulated tempering with fast on-the-fly weight determination.

scientific article published in February 2013

Computational analysis for selectivity of histone deacetylase inhibitor by replica-exchange umbrella sampling molecular dynamics simulations

article

Conformational changes of ubiquitin under high pressure conditions: A pressure simulated tempering molecular dynamics study

scientific article published on 8 April 2017

Conformational dynamics of oligosaccharides characterized by paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics simulation

scientific article published on January 2015

Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fcγ receptor IIIa

scientific article

Conformational properties of an artificial GM1 glycan cluster based on a metal-ligand complex

article

Constraint on ’t Hooft indices in preon models with complementarity

scientific article published on 01 December 1986

Cooperative folding mechanism of a β-hairpin peptide studied by a multicanonical replica-exchange molecular dynamics simulation

article

Dependency of ligand free energy landscapes on charge parameters and solvent models

Determination of the structural ensemble of the molten globule state of a protein by computer simulations

scientific article published on 24 April 2019

Distribution and Structure Analysis of Fibril-Forming Peptides Focusing on Concentration Dependency

scientific article published in 2022

Drug design by generalized-ensemble simulations.

scientific article published on January 2011

Effective sampling in the configurational space of a small peptide by the multicanonical-multioverlap algorithm.

scientific article published on 22 August 2007

Eighth-order QED contribution to the anomalous magnetic moment of the muon

scientific article published on 01 January 1990

Enhanced sampling method in molecular simulations using genetic algorithm for biomolecular systems

scientific article published on 10 November 2018

Equilibrium molecular thermodynamics from Kirkwood sampling

scientific article published on 12 May 2015

Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isobaric-isothermal, and related ensembles

scientific article

Exploration of Conformational Spaces of High-Mannose-Type Oligosaccharides by an NMR-Validated Simulation

scientific article published on 04 September 2014

Folding simulations of gramicidin A into the beta-helix conformations: Simulated annealing molecular dynamics study

article

Free energy calculations for DNA base stacking by replica-exchange umbrella sampling

Free-energy analyses of a proton transfer reaction by simulated-tempering umbrella sampling and first-principles molecular dynamics simulations ⬇️

scientific article published on February 4, 2013

From multidimensional replica-exchange method to multidimensional multicanonical algorithm and simulated tempering.

scientific article published on 8 April 2009

Generalized Einstein theory on solar and galactic scales

scientific article published on 01 July 1993

Generalized-ensemble Monte Carlo method for systems with rough energy landscape

Hadronic contributions to the anomalous magnetic moment of the muon

scientific article published on 01 April 1985

Helix-forming tendencies of nonpolar amino acids predicted by Monte Carlo simulated annealing

scientific article published on 01 May 1994

Hydrophobic Core Formation and Dehydration in Protein Folding Studied by Generalized-Ensemble Simulations ⬇️

scientific article published on September 8, 2010

Improvement of the backbone-torsion-energy term in the force field for protein systems by the double Fourier series expansion

MOLECULAR DYNAMICS SIMULATIONS OF DNA DIMERS BASED ON REPLICA-EXCHANGE UMBRELLA SAMPLING II: FREE ENERGY ANALYSIS

article

Modeling (15)N NMR chemical shift changes in protein backbone with pressure

scientific article

Molecular Simulations of Protein Systems toward Drug Discovery

scientific article published on 01 January 2016

Monte Carlo simulation in the isobaric-multithermal ensemble of a bulk Lennard-Jones fluid system: Thermodynamic quantities for pressure fromP∗=2.42to 7.25

scientific article published on 01 May 2008

Monte Carlo simulations in generalized ensemble: Multicanonical algorithm versus simulated tempering.

scientific article published in November 1996

Monte Carlo simulations in generalized isobaric-isothermal ensembles

scientific article published on 13 August 2004

Multibaric-multithermal ensemble molecular dynamics simulations

scientific article published in February 2006

Multidimensional generalized-ensemble algorithms for complex systems.

scientific article published in June 2009

Multidimensional replica-exchange method for free-energy calculations

Multioverlap simulations for transitions between reference configurations ⬇️

scientific article published on September 23, 2003

New Monte Carlo algorithms for protein folding.

scientific article

New approach to the first-order phase transition of Lennard-Jones fluids

scientific article published in April 2004

Observation of helix associations for insertion of a retinal molecule and distortions of helix structures in bacteriorhodopsin.

scientific article published on December 2015

Optimisation of OPLS–UA force-field parameters for protein systems using protein data bank

Optimization of protein force-field parameters with the Protein Data Bank

article by Yoshitake Sakae & Yuko Okamoto published December 2003 in Chemical Physics Letters

PROTEIN FORCE-FIELD PARAMETERS OPTIMIZED WITH THE PROTEIN DATA BANK I: FORCE-FIELD OPTIMIZATIONS

article by YOSHITAKE SAKAE & Yuko Okamoto published September 2004 in Journal of Theoretical and Computational Chemistry

PROTEIN FORCE-FIELD PARAMETERS OPTIMIZED WITH THE PROTEIN DATA BANK II: COMPARISONS OF FORCE FIELDS BY FOLDING SIMULATIONS OF SHORT PEPTIDES

Prediction of Ligand Binding Affinity by the Combination of Replica-Exchange Method and Double-Decoupling Method

scientific article published on 01 August 2014

Prediction of Low-Energy Structures of Met-Enkephalin by Monte Carlo Simulated Annealing

Prediction of Protein-Ligand Binding Structures by Replica-Exchange Umbrella Sampling Simulations: Application to Kinase Systems

scientific article published on 25 September 2013

Prediction of membrane protein structures by replica-exchange Monte Carlo simulations: case of two helices.

scientific article

Prediction of peptide conformation by multicanonical algorithm: New approach to the multiple-minima problem

Protein folding simulations by generalized-ensemble algorithms.

scientific article published on January 2014

Protein structure predictions by parallel simulated annealing molecular dynamics using genetic crossover.

scientific article

QM/MM free energy simulations: recent progress and challenges

scientific article published on 05 July 2016

Quantum chemical replica-exchange umbrella sampling molecular dynamics simulations reveal the formation mechanism of iron phthalocyanine from iron and phthalonitrile

scientific article published on 01 August 2018

Replica-exchange extensions of simulated tempering method

scientific article published in August 2004

Replica-exchange method in van der Waals radius space: overcoming steric restrictions for biomolecules.

scientific article published in April 2010

Replica-exchange molecular dynamics method for protein folding

article

Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape

Residual entropy of ordinary ice calculated from multicanonical Monte Carlo simulations

Salt effects on hydrophobic-core formation in folding of a helical miniprotein studied by molecular dynamics simulations.

scientific article published on 6 December 2013

Secondary-Structure Design of Proteins by a Backbone Torsion Energy

article by Yoshitake Sakae & Yuko Okamoto published 15 May 2006 in Journal of the Physical Society of Japan

Simulated tempering and magnetizing: application of two-dimensional simulated tempering to the two-dimensional Ising model and its crossover.

scientific article published on 9 November 2012

Structures of a peptide fragment of beta2-microglobulin studied by replica-exchange molecular dynamics simulations - towards the understanding of the mechanism of amyloid formation

scientific article published in October 2005

Temperature dependence of distributions of conformations of a small peptide.

scientific article published in August 1998

Thermodynamic perspective on the dock-lock growth mechanism of amyloid fibrils.

scientific article

Thermodynamics of two lattice ice models in three dimensions

scientific article published on 13 October 2008

List of works by Yuko Okamoto

A pH-dependent variation in alpha-helix structure of the S-peptide of ribonuclease A studied by Monte Carlo simulated annealing

A prediction of tertiary structures of peptide by the Monte Carlo simulated annealing method.

Ab Initio prediction of protein-ligand binding structures by replica-exchange umbrella sampling simulations

Amino-acid-dependent main-chain torsion-energy terms for protein systems

Amyloid-beta(29-42) dimer formations studied by a multicanonical-multioverlap molecular dynamics simulation.

Analysis of helix-helix interactions of bacteriorhodopsin by replica-exchange simulations

Beta-sheet folding of fragment (16-36) of bovine pancreatic trypsin inhibitor as predicted by Monte Carlo simulated annealing

Characteristic temperatures of folding of a small peptide ⬇️

Classification and Prediction of Low-Energy Membrane Protein Helix Configurations by Replica-Exchange Monte Carlo Method

Classification of Low-Energy Conformations of Met-Enkephalin in the Gas Phase and in a Model Solvent Based on the Extended Scaled Particle Theory

Communication: Simulated tempering with fast on-the-fly weight determination.

Computational analysis for selectivity of histone deacetylase inhibitor by replica-exchange umbrella sampling molecular dynamics simulations

Conformational changes of ubiquitin under high pressure conditions: A pressure simulated tempering molecular dynamics study

Conformational dynamics of oligosaccharides characterized by paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics simulation

Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fcγ receptor IIIa

Conformational properties of an artificial GM1 glycan cluster based on a metal-ligand complex

Constraint on ’t Hooft indices in preon models with complementarity

Cooperative folding mechanism of a β-hairpin peptide studied by a multicanonical replica-exchange molecular dynamics simulation

Dependency of ligand free energy landscapes on charge parameters and solvent models

Determination of the structural ensemble of the molten globule state of a protein by computer simulations

Distribution and Structure Analysis of Fibril-Forming Peptides Focusing on Concentration Dependency

Drug design by generalized-ensemble simulations.

Effective sampling in the configurational space of a small peptide by the multicanonical-multioverlap algorithm.

Eighth-order QED contribution to the anomalous magnetic moment of the muon

Enhanced sampling method in molecular simulations using genetic algorithm for biomolecular systems

Equilibrium molecular thermodynamics from Kirkwood sampling

Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isobaric-isothermal, and related ensembles

Exploration of Conformational Spaces of High-Mannose-Type Oligosaccharides by an NMR-Validated Simulation

Folding simulations of gramicidin A into the beta-helix conformations: Simulated annealing molecular dynamics study

Free energy calculations for DNA base stacking by replica-exchange umbrella sampling

Free-energy analyses of a proton transfer reaction by simulated-tempering umbrella sampling and first-principles molecular dynamics simulations ⬇️

From multidimensional replica-exchange method to multidimensional multicanonical algorithm and simulated tempering.

Generalized Einstein theory on solar and galactic scales

Generalized-ensemble Monte Carlo method for systems with rough energy landscape

Hadronic contributions to the anomalous magnetic moment of the muon

Helix-forming tendencies of nonpolar amino acids predicted by Monte Carlo simulated annealing

Hydrophobic Core Formation and Dehydration in Protein Folding Studied by Generalized-Ensemble Simulations ⬇️

Improvement of the backbone-torsion-energy term in the force field for protein systems by the double Fourier series expansion

MOLECULAR DYNAMICS SIMULATIONS OF DNA DIMERS BASED ON REPLICA-EXCHANGE UMBRELLA SAMPLING II: FREE ENERGY ANALYSIS

Modeling (15)N NMR chemical shift changes in protein backbone with pressure

Molecular Simulations of Protein Systems toward Drug Discovery

Monte Carlo simulation in the isobaric-multithermal ensemble of a bulk Lennard-Jones fluid system: Thermodynamic quantities for pressure fromP∗=2.42to 7.25

Monte Carlo simulations in generalized ensemble: Multicanonical algorithm versus simulated tempering.

Monte Carlo simulations in generalized isobaric-isothermal ensembles

Multibaric-multithermal ensemble molecular dynamics simulations

Multidimensional generalized-ensemble algorithms for complex systems.

Multidimensional replica-exchange method for free-energy calculations

Multioverlap simulations for transitions between reference configurations ⬇️

New Monte Carlo algorithms for protein folding.

New approach to the first-order phase transition of Lennard-Jones fluids

Observation of helix associations for insertion of a retinal molecule and distortions of helix structures in bacteriorhodopsin.

Optimisation of OPLS–UA force-field parameters for protein systems using protein data bank

Optimization of protein force-field parameters with the Protein Data Bank

PROTEIN FORCE-FIELD PARAMETERS OPTIMIZED WITH THE PROTEIN DATA BANK I: FORCE-FIELD OPTIMIZATIONS

PROTEIN FORCE-FIELD PARAMETERS OPTIMIZED WITH THE PROTEIN DATA BANK II: COMPARISONS OF FORCE FIELDS BY FOLDING SIMULATIONS OF SHORT PEPTIDES

Prediction of Ligand Binding Affinity by the Combination of Replica-Exchange Method and Double-Decoupling Method

Prediction of Low-Energy Structures of Met-Enkephalin by Monte Carlo Simulated Annealing

Prediction of Protein-Ligand Binding Structures by Replica-Exchange Umbrella Sampling Simulations: Application to Kinase Systems

Prediction of membrane protein structures by replica-exchange Monte Carlo simulations: case of two helices.

Prediction of peptide conformation by multicanonical algorithm: New approach to the multiple-minima problem

Protein folding simulations by generalized-ensemble algorithms.

Protein structure predictions by parallel simulated annealing molecular dynamics using genetic crossover.

QM/MM free energy simulations: recent progress and challenges

Quantum chemical replica-exchange umbrella sampling molecular dynamics simulations reveal the formation mechanism of iron phthalocyanine from iron and phthalonitrile

Replica-exchange extensions of simulated tempering method

Replica-exchange method in van der Waals radius space: overcoming steric restrictions for biomolecules.

Replica-exchange molecular dynamics method for protein folding

Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape

Residual entropy of ordinary ice calculated from multicanonical Monte Carlo simulations

Salt effects on hydrophobic-core formation in folding of a helical miniprotein studied by molecular dynamics simulations.

Secondary-Structure Design of Proteins by a Backbone Torsion Energy

Simulated tempering and magnetizing: application of two-dimensional simulated tempering to the two-dimensional Ising model and its crossover.

Structures of a peptide fragment of beta2-microglobulin studied by replica-exchange molecular dynamics simulations - towards the understanding of the mechanism of amyloid formation

Temperature dependence of distributions of conformations of a small peptide.

Thermodynamic perspective on the dock-lock growth mechanism of amyloid fibrils.

Thermodynamics of two lattice ice models in three dimensions

Two-dimensional replica-exchange method for predicting protein-ligand binding structures