Yuko Okamoto

发表

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

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

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

Yuko Okamoto, Yoshiharu Mori, 2017, J. Comput. Chem..

Monte-Carlo Simulated Annealing in Protein Folding

Yuko Okamoto, 2009, Encyclopedia of Optimization.

Implementation of replica-exchange umbrella sampling in the DFTB+ semiempirical quantum chemistry package

Yuko Okamoto, Stephan Irle, Shingo Ito, 2016, Comput. Phys. Commun..

Implementation of replica-exchange umbrella sampling in GAMESS

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

Molecular dynamics simulations in the multibaric–multithermal ensemble

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

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

Yuko Okamoto, Toshimasa Tanaka, Hironori Kokubo, 2011, J. Comput. Chem..

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

Yuko Okamoto, Tomoyuki Hiroyasu, Mitsunori Miki, 2011, J. Comput. Chem..

A new generalized-ensemble algorithm: multicanonical–multioverlap algorithm

Yuko Okamoto, Satoru G. Itoh, 2007 .

Generalized-Ensemble Algorithms for Simulations of Complex Molecular Systems

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

New Conformational Search Method Using Genetic Algorithm and Knot Theory for Proteins

Yuko Okamoto, Tomoyuki Hiroyasu, Mitsunori Miki, 2011, Pacific Symposium on Biocomputing.

Multibaric–multithermal ensemble molecular dynamics simulations

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

Generalized-ensemble algorithms for molecular dynamics simulations

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

Generalized‐Ensemble Monte Carlo Algorithms for Simulations of Proteins

Yuko Okamoto, Yuji Sugita, Ayori Mitsutake, 2004 .

Deterministic replica-exchange method without pseudo random numbers for simulations of complex systems

Yuko Okamoto, Ryo Urano, 2015, Comput. Phys. Commun..

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

Yuko Okamoto, John E. Straub, Yoshitake Sakae, 2019, J. Comput. Chem..

Generalized-ensemble algorithms for protein folding simulations

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

Enhanced sampling algorithms.

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

Multi-overlap molecular dynamics methods for biomolecular systems

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

Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations.

Yuko Okamoto, Y. Okamoto, 2003, Journal of molecular graphics & modelling.

Molecular simulations in generalised ensemble

Yuko Okamoto, 2012 .

Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. II. Application to a more complex system

Yuko Okamoto, Ayori Mitsutake, Yuji Sugita, 2003 .

Mega Process Genetic Algorithm Using Grid MP

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

Comparative Study of Multicanonical and Simulated Annealing Algorithms in the Protein Folding Problem

Yuko Okamoto, Ulrich H.E. Hansmann, 1994 .

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

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

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..

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

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

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

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

Molecular simulations in the multibaric-multithermal ensembles

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

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..

Drug design by generalized-ensemble simulations.

Yuko Okamoto, 2011, Current pharmaceutical design.

Replica-exchange extensions of simulated tempering method.

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

Comment on "Monte Carlo Simulation of a First-Order Transition"

Yuko Okamoto, Bernd A. Berg, Ulrich H.E. Hansmann, 1994 .

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

Yuko Okamoto, Ayori Mitsutake, 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

α-Helix Propensities of Amino Acids Studied by Multicanonical Algorithm

Yuko Okamoto, Ulrich H. E. Hansmann, Takashi Nakazawa, 1995 .

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.

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.

Hydrophobic core formation and dehydration in protein folding studied by generalized-ensemble simulations.

Yuko Okamoto, Yuji Sugita, Takao Yoda, 2010, Biophysical journal.

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.

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.

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

Yuko Okamoto, Masahiro Kinoshita, Fumio Hirata, 1998 .

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

Yuko Okamoto, Yukio Kawashima, Yuji Sugita, 2005 .

An Analysis on Protein Folding Problem by Replica-Exchange Method

Yuko Okamoto, Yuji Sugita, 2000 .

Replica-exchange Monte Carlo method for the isobaric isothermal ensemble

Yuko Okamoto, Masuhiro Mikami, Masaaki Kawata, 2001 .

The Generalized-Ensemble Approach for Protein Folding Simulations

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

Multidimensional generalized-ensemble algorithms for complex systems.

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

Prediction of transmembrane helix configurations by replica-exchange simulations

Yuko Okamoto, Hironori Kokubo, Y. Okamoto, 2003, cond-mat/0309338.

Liquid-Gas Phase Transitions Studied by Multibaric-Multithermal Monte Carlo Simulations

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

Replica-Exchange Monte Carlo Method for Ar Fluid

Yuko Okamoto, Takeshi Nishikawa, Masuhiro Mikami, 2000 .

Combination of genetic crossover and replica-exchange method for conformational search of protein systems

Yuko Okamoto, Tomoyuki Hiroyasu, Mitsunori Miki, 2015 .

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

Yuko Okamoto, Masahiro Kinoshita, Fumio Hirata, 1998 .

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

Yuko Okamoto, Masahiro Kinoshita, Fumio Hirata, 1997 .

Monte Carlo simulations in generalized isobaric-isothermal ensembles.

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

α-Helix propensities of homo-oligomers in aqueous solution studied by multicanonical algorithm

Yuko Okamoto, Ayori Mitsutake, 1999 .

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.

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

Yuko Okamoto, Takeshi Kikuchi, Hikaru Kawai, 1992 .

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

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

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.

Ligand docking simulations by generalized-ensemble algorithms.

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

TACKLING THE PROTEIN FOLDING PROBLEM BY A GENERALIZED-ENSEMBLE APPROACH WITH TSALLIS STATISTICS

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

Explicit Symplectic Integrators of Molecular Dynamics Algorithms for Rigid-Body Molecules in the Canonical, Isothermal-Isobaric, and Related Ensembles

Yuko Okamoto, Hisashi Okumura, Satoru G. Itoh, 2006 .

Secondary-structure preferences of force fields for proteins evaluated by generalized-ensemble simulations

Yuko Okamoto, Yuji Sugita, Takao Yoda, 2004 .

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

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

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

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

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

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

Combination of the Replica-Exchange Monte Carlo Method and the Reference Interaction Site Model Theory for Simulating a Peptide Molecule in Aqueous Solution

Yuko Okamoto, Fumio Hirata, Ayori Mitsutake, 2004 .

Helix-Hairpin Transitions of a Designed Peptide Studied by a Generalized-Ensemble Simulation

Yuko Okamoto, Satoru G. Itoh, Atsuo Tamura, 2010 .

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 .

Multicanonical algorithm combined with the RISM theory for simulating peptides in aqueous solution

Yuko Okamoto, Masahiro Kinoshita, Fumio Hirata, 2000 .

Effects of Side-Chain Charges on α-Helix Stability in C-Peptide of Ribonuclease A Studied by Multicanonical Algorithm

Yuko Okamoto, Ulrich H. E. Hansmann† and, 1999 .

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.

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.

A novel algorithm for calculation of the extreme eigenvalues of large Hermitian matrices

Yuko Okamoto, Humphrey J. Maris, 1993 .

Conformational search simulations of Trp-cage using genetic crossover

Yuko Okamoto, Tomoyuki Hiroyasu, Mitsunori Miki, 2015 .

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

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

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

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

Optimizations of Protein Force Fields

Yuko Okamoto, Yoshitake Sakae, Y. Okamoto, 2012, Springer Series on Bio- and Neurosystems.

Generalized-Ensemble Algorithms for Studying Protein Folding

Yuko Okamoto, Y. Okamoto, 2009 .

Protein folding simulations and structure predictions

Yuko Okamoto, Y. Okamoto, 2001 .

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.

A Conformational Search Method for Protein Systems Using Genetic Crossover and Metropolis Criterion

Yuko Okamoto, Tomoyuki Hiroyasu, Mitsunori Miki, 2014, 1505.05709.

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

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

Analysis on conformational stability of C-peptide of ribonuclease A in water using the reference interaction site model theory and Monte Carlo simulated annealing

Yuko Okamoto, Masahiro Kinoshita, Fumio Hirata, 1999 .

Replica-Exchange Molecular Dynamics Simulations for Various Constant Temperature Algorithms

Yuko Okamoto, Yoshiharu Mori, Y. Okamoto, 2010 .

Generalized-Ensemble Algorithms for the Isobaric–Isothermal Ensemble

Yuko Okamoto, Yoshiharu Mori, Y. Okamoto, 2010, 1004.2076.

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

Yuko Okamoto, Hironori Kokubo, 2009, Biophysical journal.

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.

QM/MM free energy simulations: recent progress and challenges

Yuko Okamoto, Shingo Ito, Victor Ovchinnikov, 2016, Molecular simulation.

Metropolis Algorithms in Generalized Ensemble

Yuko Okamoto, 2003 .

Residual entropy of ordinary ice from multicanonical simulations

Yuko Okamoto, Bernd A. Berg, Y. Okamoto, 2006, cond-mat/0609211.