Prediction of peptide conformation by multicanonical algorithm: New approach to the multiple-minima problem. - Ulrich H. E. Hansmann; Yuko Okamoto (J. Comput. Chem., 1993)

Numerical comparisons of three recently proposed algorithms in the protein folding problem. - Ulrich H. E. Hansmann; Yuko Okamoto (J. Comput. Chem., 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)

Calculation of solvation free energy using RISM theory for peptide in salt solution. - Masahiro Kinoshita; Yuko Okamoto; Fumio Hirata (J. Comput. Chem., 1998)

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 (IEEE Congress on Evolutionary Computation, 2003)

Mega Process Genetic Algorithm Using Grid MP. - Yoshiko Hanada; Tomoyuki Hiroyasu; Mitsunori Miki; Yuko Okamoto (LSGRID, 2004)

Molecular simulations in the multibaric-multithermal ensembles. - Hisashi Okumura; Yuko Okamoto (Comput. Phys. Commun., 2005)

Multibaric-multithermal ensemble molecular dynamics simulations. - Hisashi Okumura; Yuko Okamoto (J. Comput. Chem., 2006)

Monte-Carlo Simulated Annealing in Protein Folding. - Yuko Okamoto (Encyclopedia of Optimization, 2009)

Dependency of ligand free energy landscapes on charge parameters and solvent models. - Yuko Okamoto; Toshimasa Tanaka; Hironori Kokubo (J. Comput. Aided Mol. Des., 2010)

New Conformational Search Method Using Genetic Algorithm and Knot Theory for Proteins. - Yoshitake Sakae; Tomoyuki Hiroyasu; Mitsunori Miki; Yuko Okamoto (Pacific Symposium on Biocomputing, 2011)

Ab Initio prediction of protein-ligand binding structures by replica-exchange umbrella sampling simulations. - Hironori Kokubo; Toshimasa Tanaka; Yuko Okamoto (J. Comput. Chem., 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)

Two-dimensional replica-exchange method for predicting protein-ligand binding structures. - Hironori Kokubo; Toshimasa Tanaka; Yuko Okamoto (J. Comput. Chem., 2013)

Designed-walk replica-exchange method for simulations of complex systems. - Ryo Urano; Yuko Okamoto (Comput. Phys. Commun., 2015)

Deterministic replica-exchange method without pseudo random numbers for simulations of complex systems. - Ryo Urano; Yuko Okamoto (Comput. Phys. Commun., 2015)

Implementation of replica-exchange umbrella sampling in the DFTB+ semiempirical quantum chemistry package. - Shingo Ito; Stephan Irle; Yuko Okamoto (Comput. Phys. Commun., 2016)

Conformational changes of ubiquitin under high pressure conditions: A pressure simulated tempering molecular dynamics study. - Yoshiharu Mori; Yuko Okamoto (J. Comput. Chem., 2017)

Implementation of replica-exchange umbrella sampling in GAMESS. - Shingo Ito; Dmitri G. Fedorov; Yuko Okamoto; Stephan Irle (Comput. Phys. Commun., 2018)

Enhanced sampling method in molecular simulations using genetic algorithm for biomolecular systems. - Yoshitake Sakae; John E. Straub; Yuko Okamoto (J. Comput. Chem., 2019)

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)