Yuko Okamoto

Publication Activity (10 Years)

Years Active: 1993-2023
Publications (10 Years): 5

Top Topics

Pseudo Random Number

Complex Systems

Implementation Details

Top Venues

Comput. Phys. Commun.

J. Comput. Chem.

Publications

Hirokazu Mishima, Yukihiro Itoh, Takashi Kurohara, Takayoshi Suzuki, Naoya Asada, Ken-ichi Kusakabe, Yuko Okamoto
Origin of the kinetic HDAC2-selectivity of an HDAC inhibitor. J. Comput. Chem. 44 (18) (2023)
Yoshitake Sakae, John E. Straub, Yuko Okamoto
Enhanced sampling method in molecular simulations using genetic algorithm for biomolecular systems. J. Comput. Chem. 40 (2) (2019)
Shingo Ito, Dmitri G. Fedorov, Yuko Okamoto, Stephan Irle
Implementation of replica-exchange umbrella sampling in GAMESS. Comput. Phys. Commun. 228 (2018)
Yoshiharu Mori, Yuko Okamoto
Conformational changes of ubiquitin under high pressure conditions: A pressure simulated tempering molecular dynamics study. J. Comput. Chem. 38 (15) (2017)
Shingo Ito, Stephan Irle, Yuko Okamoto
Implementation of replica-exchange umbrella sampling in the DFTB+ semiempirical quantum chemistry package. Comput. Phys. Commun. 204 (2016)
Ryo Urano, Yuko Okamoto
Deterministic replica-exchange method without pseudo random numbers for simulations of complex systems. Comput. Phys. Commun. 197 (2015)
Ryo Urano, Yuko Okamoto
Designed-walk replica-exchange method for simulations of complex systems. Comput. Phys. Commun. 196 (2015)
Hironori Kokubo, Toshimasa Tanaka, Yuko Okamoto
Two-dimensional replica-exchange method for predicting protein-ligand binding structures. J. Comput. Chem. 34 (30) (2013)
Yoshitake Sakae, Tomoyuki Hiroyasu, Mitsunori Miki, Yuko Okamoto
New Conformational Search Method Using Genetic Algorithm and Knot Theory for Proteins. Pacific Symposium on Biocomputing (2011)
Hironori Kokubo, Toshimasa Tanaka, Yuko Okamoto
prediction of protein-ligand binding structures by replica-exchange umbrella sampling simulations. J. Comput. Chem. 32 (13) (2011)
Yoshitake Sakae, Tomoyuki Hiroyasu, Mitsunori Miki, Yuko Okamoto
Protein structure predictions by parallel simulated annealing molecular dynamics using genetic crossover. J. Comput. Chem. 32 (7) (2011)
Yuko Okamoto, Toshimasa Tanaka, Hironori Kokubo
Dependency of ligand free energy landscapes on charge parameters and solvent models. J. Comput. Aided Mol. Des. 24 (8) (2010)
Hisashi Okumura, Yuko Okamoto
Multibaric-multithermal ensemble molecular dynamics simulations. J. Comput. Chem. 27 (3) (2006)
Hisashi Okumura, Yuko Okamoto
Molecular simulations in the multibaric-multithermal ensembles. Comput. Phys. Commun. 169 (1-3) (2005)
Yoshiko Hanada, Tomoyuki Hiroyasu, Mitsunori Miki, Yuko Okamoto
Mega Process Genetic Algorithm Using Grid MP. LSGRID (2004)
S. Ogura, K. Aoi, Tomoyuki Hiroyasu, Mitsunori Miki, Yuko Okamoto
Energy minimization of protein tertiary structures by local search algorithm and parallel simulated annealing using genetic crossover. IEEE Congress on Evolutionary Computation (2003)
Masahiro Kinoshita, Yuko Okamoto, Fumio Hirata
Calculation of solvation free energy using RISM theory for peptide in salt solution. J. Comput. Chem. 19 (15) (1998)
Ulrich H. E. Hansmann, Yuko Okamoto
Numerical comparisons of three recently proposed algorithms in the protein folding problem. J. Comput. Chem. 18 (7) (1997)
Masahiro Kinoshita, Yuko Okamoto, Fumio Hirata
Calculation of hydration free energy for a solute with many atomic sites using the RISM theory: A robust and efficient algorithm. J. Comput. Chem. 18 (10) (1997)
Ulrich H. E. Hansmann, Yuko Okamoto
Prediction of peptide conformation by multicanonical algorithm: New approach to the multiple-minima problem. J. Comput. Chem. 14 (11) (1993)