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2020 – today
- 2023
[j17]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): 1604-1609 (2023)
2010 – 2019
- 2019
- [j16]Yoshitake Sakae, John E. Straub, Yuko Okamoto:
Enhanced sampling method in molecular simulations using genetic algorithm for biomolecular systems. J. Comput. Chem. 40(2): 475-481 (2019) - 2018
- [j15]Shingo Ito, Dmitri G. Fedorov, Yuko Okamoto, Stephan Irle:
Implementation of replica-exchange umbrella sampling in GAMESS. Comput. Phys. Commun. 228: 152-162 (2018) - 2017
- [j14]Yoshiharu Mori, Yuko Okamoto:
Conformational changes of ubiquitin under high pressure conditions: A pressure simulated tempering molecular dynamics study. J. Comput. Chem. 38(15): 1167-1173 (2017) - 2016
- [j13]Shingo Ito, Stephan Irle, Yuko Okamoto:
Implementation of replica-exchange umbrella sampling in the DFTB+ semiempirical quantum chemistry package. Comput. Phys. Commun. 204: 1-10 (2016) - 2015
- [j12]Ryo Urano, Yuko Okamoto:
Designed-walk replica-exchange method for simulations of complex systems. Comput. Phys. Commun. 196: 380-383 (2015) - [j11]Ryo Urano, Yuko Okamoto:
Deterministic replica-exchange method without pseudo random numbers for simulations of complex systems. Comput. Phys. Commun. 197: 128-135 (2015) - 2013
- [j10]Hironori Kokubo, Toshimasa Tanaka, Yuko Okamoto:
Two-dimensional replica-exchange method for predicting protein-ligand binding structures. J. Comput. Chem. 34(30): 2601-2614 (2013) - 2011
- [j9]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): 1353-1360 (2011) - [j8]Hironori Kokubo, Toshimasa Tanaka, Yuko Okamoto:
Ab Initio prediction of protein-ligand binding structures by replica-exchange umbrella sampling simulations. J. Comput. Chem. 32(13): 2810-2821 (2011) - [c3]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: 217-228 - 2010
- [j7]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): 699-712 (2010)
2000 – 2009
- 2009
- [r1]Yuko Okamoto:
Monte-Carlo Simulated Annealing in Protein Folding. Encyclopedia of Optimization 2009: 2323-2337 - 2006
- [j6]Hisashi Okumura, Yuko Okamoto:
Multibaric-multithermal ensemble molecular dynamics simulations. J. Comput. Chem. 27(3): 379-395 (2006) - 2005
- [j5]Hisashi Okumura, Yuko Okamoto:
Molecular simulations in the multibaric-multithermal ensembles. Comput. Phys. Commun. 169(1-3): 317-321 (2005) - 2004
- [c2]Yoshiko Hanada, Tomoyuki Hiroyasu, Mitsunori Miki, Yuko Okamoto:
Mega Process Genetic Algorithm Using Grid MP. LSGRID 2004: 152-170 - 2003
- [c1]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: 1933-1940
1990 – 1999
- 1998
- [j4]Masahiro Kinoshita, Yuko Okamoto, Fumio Hirata:
Calculation of solvation free energy using RISM theory for peptide in salt solution. J. Comput. Chem. 19(15): 1724-1735 (1998) - 1997
- [j3]Ulrich H. E. Hansmann, Yuko Okamoto:
Numerical comparisons of three recently proposed algorithms in the protein folding problem. J. Comput. Chem. 18(7): 920-933 (1997) - [j2]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): 1320-1326 (1997) - 1993
- [j1]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): 1333-1338 (1993)
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