Yuko Okamoto - researchr alias

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2023

Origin of the kinetic HDAC2-selectivity of an HDAC inhibitorHirokazu Mishima, Yukihiro Itoh, Takashi Kurohara, Takayoshi Suzuki, Naoya Asada, Ken-ichi Kusakabe, Yuko Okamoto. jcc, 44(18):1604-1609, 2023. [doi]

2019

Enhanced sampling method in molecular simulations using genetic algorithm for biomolecular systemsYoshitake Sakae, John E. Straub, Yuko Okamoto. jcc, 40(2):475-481, 2019. [doi]

2018

Implementation of replica-exchange umbrella sampling in GAMESSShingo Ito, Dmitri G. Fedorov, Yuko Okamoto, Stephan Irle. cphysics, 228:152-162, 2018. [doi]

2017

Conformational changes of ubiquitin under high pressure conditions: A pressure simulated tempering molecular dynamics studyYoshiharu Mori, Yuko Okamoto. jcc, 38(15):1167-1173, 2017. [doi]

2016

Implementation of replica-exchange umbrella sampling in the DFTB+ semiempirical quantum chemistry packageShingo Ito, Stephan Irle, Yuko Okamoto. cphysics, 204:1-10, 2016. [doi]

2015

Designed-walk replica-exchange method for simulations of complex systemsRyo Urano, Yuko Okamoto. cphysics, 196:380-383, 2015. [doi]

Deterministic replica-exchange method without pseudo random numbers for simulations of complex systemsRyo Urano, Yuko Okamoto. cphysics, 197:128-135, 2015. [doi]

2013

Two-dimensional replica-exchange method for predicting protein-ligand binding structuresHironori Kokubo, Toshimasa Tanaka, Yuko Okamoto. jcc, 34(30):2601-2614, 2013. [doi]

2011

2010

Dependency of ligand free energy landscapes on charge parameters and solvent modelsYuko Okamoto, Toshimasa Tanaka, Hironori Kokubo. jcamd, 24(8):699-712, 2010. [doi]

2006

Multibaric-multithermal ensemble molecular dynamics simulationsHisashi Okumura, Yuko Okamoto. jcc, 27(3):379-395, 2006. [doi]

2005

Molecular simulations in the multibaric-multithermal ensemblesHisashi Okumura, Yuko Okamoto. cphysics, 169(1-3):317-321, 2005. [doi]

2004

Mega Process Genetic Algorithm Using Grid MPYoshiko Hanada, Tomoyuki Hiroyasu, Mitsunori Miki, Yuko Okamoto. lsgrid 2005: 152-170 [doi]

2003

Energy minimization of protein tertiary structures by local search algorithm and parallel simulated annealing using genetic crossoverS. Ogura, K. Aoi, Tomoyuki Hiroyasu, Mitsunori Miki, Yuko Okamoto. cec 2003: 1933-1940 [doi]

1998

Calculation of solvation free energy using RISM theory for peptide in salt solutionMasahiro Kinoshita, Yuko Okamoto, Fumio Hirata. jcc, 19(15):1724-1735, 1998. [doi]

1997

Numerical comparisons of three recently proposed algorithms in the protein folding problemUlrich H. E. Hansmann, Yuko Okamoto. jcc, 18(7):920-933, 1997. [doi]

Calculation of hydration free energy for a solute with many atomic sites using the RISM theory: A robust and efficient algorithmMasahiro Kinoshita, Yuko Okamoto, Fumio Hirata. jcc, 18(10):1320-1326, 1997. [doi]

1993

Prediction of peptide conformation by multicanonical algorithm: New approach to the multiple-minima problemUlrich H. E. Hansmann, Yuko Okamoto. jcc, 14(11):1333-1338, 1993. [doi]

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