Yuko Okamoto

20 papers B 1Misc 1Journal 16Unranked 1
YearRankTypeTitle / Venue / Authors
2023 J jnl
Origin of the kinetic HDAC2-selectivity of an HDAC inhibitor.
J. Comput. Chem.
Hirokazu Mishima, Yukihiro Itoh, Takashi Kurohara, Takayoshi Suzuki, Naoya Asada, Ken-ichi Kusakabe, Yuko Okamoto
2019 J jnl
Enhanced sampling method in molecular simulations using genetic algorithm for biomolecular systems.
J. Comput. Chem.
Yoshitake Sakae, John E. Straub, Yuko Okamoto
2018 J jnl
Implementation of replica-exchange umbrella sampling in GAMESS.
Comput. Phys. Commun.
Shingo Ito, Dmitri G. Fedorov, Yuko Okamoto, Stephan Irle
2017 J jnl
Conformational changes of ubiquitin under high pressure conditions: A pressure simulated tempering molecular dynamics study.
J. Comput. Chem.
Yoshiharu Mori, Yuko Okamoto
2016 J jnl
Implementation of replica-exchange umbrella sampling in the DFTB+ semiempirical quantum chemistry package.
Comput. Phys. Commun.
Shingo Ito, Stephan Irle, Yuko Okamoto
2015 J jnl
Designed-walk replica-exchange method for simulations of complex systems.
Comput. Phys. Commun.
Ryo Urano, Yuko Okamoto
2015 J jnl
Deterministic replica-exchange method without pseudo random numbers for simulations of complex systems.
Comput. Phys. Commun.
Ryo Urano, Yuko Okamoto
2013 J jnl
Two-dimensional replica-exchange method for predicting protein-ligand binding structures.
J. Comput. Chem.
Hironori Kokubo, Toshimasa Tanaka, Yuko Okamoto
2011 Misc conf
New Conformational Search Method Using Genetic Algorithm and Knot Theory for Proteins.
Pacific Symposium on Biocomputing
Yoshitake Sakae, Tomoyuki Hiroyasu, Mitsunori Miki, Yuko Okamoto
2011 J jnl
Protein structure predictions by parallel simulated annealing molecular dynamics using genetic crossover.
J. Comput. Chem.
Yoshitake Sakae, Tomoyuki Hiroyasu, Mitsunori Miki, Yuko Okamoto
2010 J jnl
Dependency of ligand free energy landscapes on charge parameters and solvent models.
J. Comput. Aided Mol. Des.
Yuko Okamoto, Toshimasa Tanaka, Hironori Kokubo
2009 — ch.
Monte-Carlo Simulated Annealing in Protein Folding.
Encyclopedia of Optimization
Yuko Okamoto
2006 J jnl
Multibaric-multithermal ensemble molecular dynamics simulations.
J. Comput. Chem.
Hisashi Okumura, Yuko Okamoto
2005 J jnl
Molecular simulations in the multibaric-multithermal ensembles.
Comput. Phys. Commun.
Hisashi Okumura, Yuko Okamoto
2004 — conf
Mega Process Genetic Algorithm Using Grid MP.
LSGRID
Yoshiko Hanada, Tomoyuki Hiroyasu, Mitsunori Miki, Yuko Okamoto
2003 B conf
Energy minimization of protein tertiary structures by local search algorithm and parallel simulated annealing using genetic crossover.
IEEE Congress on Evolutionary Computation
S. Ogura, K. Aoi, Tomoyuki Hiroyasu, Mitsunori Miki, Yuko Okamoto
1998 J jnl
Calculation of solvation free energy using RISM theory for peptide in salt solution.
J. Comput. Chem.
Masahiro Kinoshita, Yuko Okamoto, Fumio Hirata
1997 J jnl
Calculation of hydration free energy for a solute with many atomic sites using the RISM theory: A robust and efficient algorithm.
J. Comput. Chem.
Masahiro Kinoshita, Yuko Okamoto, Fumio Hirata
1997 J jnl
Numerical comparisons of three recently proposed algorithms in the protein folding problem.
J. Comput. Chem.
Ulrich H. E. Hansmann, Yuko Okamoto
1993 J jnl
Prediction of peptide conformation by multicanonical algorithm: New approach to the multiple-minima problem.
J. Comput. Chem.
Ulrich H. E. Hansmann, Yuko Okamoto