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Journal of Computational Chemistry|May 5, 2018
Performance evaluation of the zero-multipole summation method in modern molecular dynamics softwareShun Sakuraba, Ikuo FukudaThe Journal of Physical Chemistry. B|February 15, 2018
Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide ConformationKota Kasahara, Shun Sakuraba, Ikuo FukudaBiophysics and Physicobiology|June 12, 2025
A virtual system-coupled molecular dynamics simulation free from experimental knowledge on binding sites: Application to RNA-ligand binding free-energy landscapeJunichi Higo, Kota Kasahara, Shun Sakuraba, et al.The Journal of Chemical Physics|August 8, 2016
Comment on "Replica-exchange-with-tunneling for fast exploration of protein landscapes" [J. Chem. Phys. 143, 224102 (2015)]Shun SakurabaThe Journal of Chemical Physics|November 12, 2013
Zero-multipole summation method for efficiently estimating electrostatic interactions in molecular systemIkuo FukudaScientific Reports|August 13, 2022
Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible moleculeJunichi Higo, Kota Kasahara, Gert-Jan Bekker, et al.Journal of Computational Chemistry|December 19, 2008
Multiple Markov transition matrix method: obtaining the stationary probability distribution from multiple simulationsShun Sakuraba, Akio KitaoJournal of Computational Chemistry|June 14, 2014
Ermod: fast and versatile computation software for solvation free energy with approximate theory of solutionsShun Sakuraba, Nobuyuki MatubayasiThe Journal of Chemical Physics|September 29, 2011
Distribution-function approach to free energy computationShun Sakuraba, Nobuyuki MatubayasiThe Journal of Chemical Physics|August 22, 2016
Spotting the difference in molecular dynamics simulations of biomoleculesShun Sakuraba, Hidetoshi KonoPageof 27