Yuko Okamoto

According to our database, Yuko Okamoto authored at least 21 papers between 1993 and 2023.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2023

Origin of the kinetic HDAC2-selectivity of an HDAC inhibitor.

Hirokazu Mishima, Yukihiro Itoh, Takashi Kurohara, Takayoshi Suzuki, Naoya Asada, Ken-ichi Kusakabe, Yuko Okamoto

J. Comput. Chem., 2023

2019

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

Yoshitake Sakae, John E. Straub, Yuko Okamoto

J. Comput. Chem., 2019

2018

Implementation of replica-exchange umbrella sampling in GAMESS.

Shingo Ito, Dmitri G. Fedorov, Yuko Okamoto, Stephan Irle

Comput. Phys. Commun., 2018

2017

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

Yoshiharu Mori, Yuko Okamoto

J. Comput. Chem., 2017

2016

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

Shingo Ito, Stephan Irle, Yuko Okamoto

Comput. Phys. Commun., 2016

2015

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

Ryo Urano, Yuko Okamoto

Comput. Phys. Commun., 2015

Designed-walk replica-exchange method for simulations of complex systems.

Ryo Urano, Yuko Okamoto

Comput. Phys. Commun., 2015

2013

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

Hironori Kokubo, Toshimasa Tanaka, Yuko Okamoto

J. Comput. Chem., 2013

2011

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

Yoshitake Sakae, Tomoyuki Hiroyasu, Mitsunori Miki, Yuko Okamoto

J. Comput. Chem., 2011

<i>Ab Initio</i> prediction of protein-ligand binding structures by replica-exchange umbrella sampling simulations.

Hironori Kokubo, Toshimasa Tanaka, Yuko Okamoto

J. Comput. Chem., 2011

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

Yoshitake Sakae, Tomoyuki Hiroyasu, Mitsunori Miki, Yuko Okamoto

Proceedings of the Biocomputing 2011: Proceedings of the Pacific Symposium, 2011

2010

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

Yuko Okamoto, Toshimasa Tanaka, Hironori Kokubo

J. Comput. Aided Mol. Des., 2010

2009

Monte-Carlo Simulated Annealing in Protein Folding.

Yuko Okamoto

Proceedings of the Encyclopedia of Optimization, Second Edition, 2009

2006

Multibaric-multithermal ensemble molecular dynamics simulations.

Hisashi Okumura, Yuko Okamoto

J. Comput. Chem., 2006

2005

Molecular simulations in the multibaric-multithermal ensembles.

Hisashi Okumura, Yuko Okamoto

Comput. Phys. Commun., 2005

2004

Mega Process Genetic Algorithm Using Grid MP.

Yoshiko Hanada, Tomoyuki Hiroyasu, Mitsunori Miki, Yuko Okamoto

Proceedings of the Grid Computing in Life Science, 2004

2003

Energy minimization of protein tertiary structures by local search algorithm and parallel simulated annealing using genetic crossover.

S. Ogura, K. Aoi, Tomoyuki Hiroyasu, Mitsunori Miki, Yuko Okamoto

Proceedings of the IEEE Congress on Evolutionary Computation, 2003

1998

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

Masahiro Kinoshita, Yuko Okamoto, Fumio Hirata

J. Comput. Chem., 1998

1997

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

Masahiro Kinoshita, Yuko Okamoto, Fumio Hirata

J. Comput. Chem., 1997

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

Ulrich H. E. Hansmann, Yuko Okamoto

J. Comput. Chem., 1997

1993

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

Ulrich H. E. Hansmann, Yuko Okamoto

J. Comput. Chem., 1993