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  • Yasuhiro Matsunaga, Hiroshi Fujisaki, Tohru Terada, Tadaomi Furuta, Kei Moritsugu, Akinori Kidera
  • Computer Science, Medicine, Biology
  • PLoS Computational Biology
  • 2012 (First Publication: 1 June 2012)
  • Large-scale conformational changes in proteins involve barrier-crossing transitions on the complex free energy surfaces of high-dimensional space. Such rare events cannot be efficiently captured byExpand
  • Jaewoon Jung, Takaharu Mori, +4 authors Yuji Sugita
  • Medicine, Computer Science
  • Wiley interdisciplinary reviews. Computational…
  • 2015 (First Publication: 7 May 2015)
  • GENESIS (Generalized-Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN isExpand
  • Chigusa Kobayashi, Jaewoon Jung, +5 authors Yuji Sugita
  • Computer Science, Medicine
  • J. Comput. Chem.
  • 2017 (First Publication: 30 September 2017)
  • GENeralized-Ensemble SImulation System (GENESIS) is a software package for molecular dynamics (MD) simulation of biological systems. It is designed to extend limitations in system size and accessibleExpand
  • Gareth J Rylance, Roy L. Johnston, Yasuhiro Matsunaga, Chun-Biu Li, Akinori Baba, Tamiki Komatsuzaki
  • Medicine, Computer Science
  • Proceedings of the National Academy of Sciences
  • 2006 (First Publication: 5 December 2006)
  • A scheme for visualizing and quantifying the complexity of multidimensional energy landscapes and multiple pathways is presented employing principal component-based disconnectivity graphs and theExpand
  • Tamiki Komatsuzaki, Kyoko Hoshino, Yasuhiro Matsunaga, Gareth J Rylance, Roy L. Johnston, David J. Wales
  • Chemistry, Medicine
  • The Journal of chemical physics
  • 2005 (First Publication: 22 February 2005)
  • A scheme to approximate the multidimensional potential energy landscape in terms of a minimal number of degrees of freedom is proposed using a linear transformation of the original atomic CartesianExpand
  • Yasuhiro Matsunaga, Yasuaki Komuro, Chigusa Kobayashi, Jaewoon Jung, Takaharu Mori, Yuji Sugita
  • Medicine, Chemistry
  • The journal of physical chemistry letters
  • 2016 (First Publication: 6 April 2016)
  • Collective variables (CVs) are often used in molecular dynamics simulations based on enhanced sampling algorithms to investigate large conformational changes of a protein. The choice of CVs in theseExpand