Y. Okamoto

Y. Okamoto, M. Miki, J. Dongarra, 2004, Proceedings. Seventh International Conference on High Performance Computing and Grid in Asia Pacific Region, 2004..

N+-C-H···O Hydrogen bonds in protein-ligand complexes

Y. Okamoto, Yukihiro Itoh, Y. Nakashima, 2019, Scientific Reports.

Mega Process Genetic Algorithm Using Grid MP

Yuko Okamoto, Tomoyuki Hiroyasu, Mitsunori Miki, 2004, LSGRID.

Two‐dimensional replica‐exchange method for predicting protein–ligand binding structures

Yuko Okamoto, Toshimasa Tanaka, Hironori Kokubo, 2013, J. Comput. Chem..

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

Yuko Okamoto, Hisashi Okumura, Y. Okamoto, 2009, The Journal of chemical physics.

Multidimensional generalized-ensemble algorithms for complex systems.

Yuko Okamoto, Ayori Mitsutake, Y. Okamoto, 2009, The Journal of chemical physics.

Calculation of hydration free energy for a solute with many atomic sites using the RISM theory: A robust and efficient algorithm

Yuko Okamoto, Masahiro Kinoshita, Fumio Hirata, 1997, J. Comput. Chem..

Solvent effects on conformational stability of peptides: RISM analyses

Y. Okamoto, F. Hirata, M. Kinoshita, 2001 .

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

Yuko Okamoto, Hisashi Okumura, Y. Okamoto, 2007, The Journal of chemical physics.

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

Y. Okamoto, S. Iida, Y. Sakae, 2017, Scientific Reports.

Phase Behavior of a Lipid Bilayer System Studied by a Replica-Exchange Molecular Dynamics Simulation

Y. Okamoto, T. Nagai, R. Ueoka, 2012 .

Temperature and pressure dependence of alanine dipeptide studied by multibaric-multithermal molecular dynamics simulations.

Yuko Okamoto, Hisashi Okumura, Y. Okamoto, 2008, The journal of physical chemistry. B.

Conformational Change of Amyloid-β 40 in Association with Binding to GM1-Glycan Cluster

Y. Okamoto, H. Okumura, Yuhei Tachi, 2019, Scientific Reports.

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

Yuko Okamoto, Bernard R Brooks, John E Straub, 2009, The journal of physical chemistry. B.

Multibaric–Multithermal Molecular Dynamics Simulation of Alanine Dipeptide in Explicit Water

Yuko Okamoto, Hisashi Okumura, Y. Okamoto, 2007 .

Generalized-ensemble algorithms for molecular dynamics simulations

Yuko Okamoto, Hisashi Okumura, Satoru G. Itoh, 2007 .

Multibaric–multithermal ensemble molecular dynamics simulations

Yuko Okamoto, Hisashi Okumura, Y. Okamoto, 2006, J. Comput. Chem..

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

Y. Okamoto, H. Okumura, Yuhei Tachi, 2018, The Journal of chemical physics.

Protein structure predictions by enhanced conformational sampling methods

Y. Okamoto, 2019, Biophysics and physicobiology.

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

Toshimasa Tanaka, Hironori Kokubo, Yuko Okamoto, 2013, Journal of chemical theory and computation.

Enhanced sampling algorithms.

Yuko Okamoto, Yoshiharu Mori, Ayori Mitsutake, 2010, Methods in molecular biology.

Generalized-Ensemble Algorithms for Simulations of Complex Molecular Systems

Yuko Okamoto, Hisashi Okumura, Satoru G. Itoh, 2012 .

Molecular mechanism for stabilizing a short helical peptide studied by generalized-ensemble simulations with explicit solvent.

Yuko Okamoto, Yuji Sugita, Y. Sugita, 2005, Biophysical journal.

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

Y. Okamoto, A. Mitsutake, M. Masuya, 2002, Biopolymers.

The crystal structure of maleylacetate reductase from Rhizobium sp. strain MTP‐10005 provides insights into the reaction mechanism of enzymes in its original family

Y. Okamoto, Y. Hata, Ai Sato, 2016, Proteins.

Monte Carlo simulations in generalized isobaric-isothermal ensembles.

Yuko Okamoto, Hisashi Okumura, Y. Okamoto, 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

Molecular dynamics simulations in the multibaric–multithermal ensemble

Yuko Okamoto, Hisashi Okumura, Y. Okamoto, 2004 .

J un 2 00 3 Monte Carlo Simulations in Multibaric-Multithermal Ensemble

Y. Okamoto, H. Okumura, 2008 .

The Generalized-Ensemble Approach for Protein Folding Simulations

Yuko Okamoto, Ulrich H. E. Hansmann, Y. Okamoto, 1999 .

MOLECULAR DYNAMICS SIMULATIONS OF DNA DIMERS BASED ON REPLICA-EXCHANGE UMBRELLA SAMPLING I: TEST OF SAMPLING EFFICIENCY

Y. Sugita, Y. Okamoto, K. Murata, 2005 .

Generalized-ensemble algorithms for protein folding simulations

Yuko Okamoto, Yuji Sugita, Ayori Mitsutake, 2007, 0707.3382.

Replica-exchange molecular dynamics simulation of diffracted X-ray tracking

Y. Sugita, Y. Okamoto, T. Yoda, 2007 .

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

Yuko Okamoto, Yuji Sugita, Takao Yoda, 2006, Proteins.

Effects of the fixed end in single-molecule imaging techniques: A replica-exchange molecular dynamics simulation study

Yuko Okamoto, Yukio Kawashima, Yuji Sugita, 2005 .

Structures of a peptide fragment of β2‐microglobulin studied by replica‐exchange molecular dynamics simulations – Towards the understanding of the mechanism of amyloid formation

Yuko Okamoto, Yuji Sugita, Takao Yoda, 2005, FEBS letters.

Optimizations of Protein Force-Field Parameters with Protein Data Bank

Y. Okamoto, Y. Sakae, 2005 .

Tertiary Structure Prediction of C-Peptide of Ribonuclease A by Multicanonical Algorithm

Yuko Okamoto, Ulrich H.E. Hansmann, Y. Okamoto, 1998, physics/9806017.

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

Yuko Okamoto, Ulrich H. E. Hansmann, Y. Okamoto, 1993, J. Comput. Chem..

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

Yuko Okamoto, Toshimasa Tanaka, Hironori Kokubo, 2010, J. Comput. Aided Mol. Des..

Ligand docking simulations by generalized-ensemble algorithms.

Yuko Okamoto, Hironori Kokubo, Y. Okamoto, 2013, Advances in protein chemistry and structural biology.

Molecular Dynamics Simulations to Clarify the Concentration Dependency of Protein Aggregation

Y. Okamoto, Y. Sakae, N. Nishikawa, 2015 .

Singular behavior of the reference interaction site model theory observed for peptide in salt solution

Y. Okamoto, F. Hirata, M. Kinoshita, 1998 .

Calculation of solvation free energy using RISM theory for peptide in salt solution

Yuko Okamoto, Masahiro Kinoshita, Fumio Hirata, 1998, J. Comput. Chem..

Implementation of replica-exchange umbrella sampling in GAMESS

Yuko Okamoto, Stephan Irle, Shingo Ito, 2018, Comput. Phys. Commun..

Conformational Change of Amyloid-β 40 in Association with Binding to GM1-Glycan Cluster

Y. Okamoto, H. Okumura, Yuhei Tachi, 2019, Scientific Reports.

Application of simulated tempering and magnetizing to a two-dimensional Potts model

Yuko Okamoto, Y. Okamoto, W. Janke, 2012, 1212.3084.

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

Yuko Okamoto, Y. Okamoto, T. Nagai, 2012, Physical review. E, Statistical, nonlinear, and soft matter physics.

Theoretical studies of transition states by the multioverlap molecular dynamics methods.

Yuko Okamoto, Y. Okamoto, S. Itoh, 2006, The Journal of chemical physics.

Multi-overlap molecular dynamics methods for biomolecular systems

Yuko Okamoto, Satoru G. Itoh, Y. Okamoto, 2004 .

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

Y. Okamoto, Y. Sakae, 2012, The Journal of chemical physics.

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

Yuko Okamoto, Hironori Kokubo, Y. Okamoto, 2014, Journal of chemical theory and computation.

Two‐dimensional replica‐exchange method for predicting protein–ligand binding structures

Y. Okamoto, H. Kokubo, Toshimasa Tanaka, 2013, J. Comput. Chem..

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

Y. Okamoto, H. Kokubo, Toshimasa Tanaka, 2011, J. Comput. Chem..

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

Y. Okamoto, H. Kokubo, Toshimasa Tanaka, 2010, J. Comput. Aided Mol. Des..

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

Y. Okamoto, H. Kokubo, 2009, Biophysical journal.

Replica-exchange methods and predictions of helix configurations of membrane proteins

Yuko Okamoto, Hironori Kokubo, Y. Okamoto, 2006 .

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

Yuko Okamoto, Philippe Derreumaux, Y. Okamoto, 2013, The Journal of chemical physics.

Solvation structure and stability of peptides in aqueous solutions analyzed by the reference interaction site model theory

Yuko Okamoto, Masahiro Kinoshita, Fumio Hirata, 1997 .

Thermodynamics of two lattice ice models in three dimensions.

Y. Okamoto, Chizuru Muguruma, Bernd A. Berg, 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

Residual entropy of ordinary ice from multicanonical simulations

Y. Okamoto, B. Berg, Chizuru Muguruma, 2006, cond-mat/0609211.

Multicanonical Algorithm, Simulated Tempering, Replica-Exchange Method, and All That

Yuko Okamoto, Ayori Mitsutake, Y. Okamoto, 2008, 0810.1117.

Molecular simulations in the multibaric-multithermal ensembles

Yuko Okamoto, Hisashi Okumura, Y. Okamoto, 2005, Comput. Phys. Commun..

Efficient simulation protocol for determining the density of states: Combination of replica-exchange Wang-Landau method and multicanonical replica-exchange method.

Y. Okamoto, T. Hayashi, 2019, Physical review. E.

Replica-exchange extensions of simulated tempering method.

Yuko Okamoto, Ayori Mitsutake, Y. Okamoto, 2004, The Journal of chemical physics.

Protein folding simulations and structure predictions

Yuko Okamoto, Y. Okamoto, 2001 .

Numerical comparisons of three recently proposed algorithms in the protein folding problem

Yuko Okamoto, Ulrich H. E. Hansmann, Y. Okamoto, 1997, J. Comput. Chem..

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

Yuko Okamoto, Satoru G. Itoh, Y. Okamoto, 2008, The journal of physical chemistry. B.

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

Y. Okamoto, Y. Sakae, T. Kawasaki, 2022, ACS omega.

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

Y. Okamoto, Ying Zhang, Y. Sakae, 2015, Advances in experimental medicine and biology.

First-Principle Determination of Peptide Conformations in Solvents: Combination of Monte Carlo Simulated Annealing and RISM Theory

Yuko Okamoto, Masahiro Kinoshita, Fumio Hirata, 1998 .

Stochastic dynamics simulations in a new generalized ensemble

Y. Okamoto, U. Hansmann, F. Eisenmenger, 1998, physics/9810052.