TOP Research Research Teams Computational Biophysics Research Team
Computational Biophysics Research Team
JapaneseTeam Leader Yuji SUGITA
- sugita[at]riken.jp (Lab location: Kobe)
- Please change [at] to @
- 2012
- Chief Scientist, RIKEN Theoretical Molecular Science Laboratory (-present)
- 2011
- Team Leader, Laboratory of Biomolecular Function Simulation, RIKEN QBiC
- 2010
- Team Leader, Computational Biophysics Research Team, AICS (renamed R-CCS in 2018), RIKEN (-present)
- 2007
- Associate Chief Scientist, RIKEN Theoretical Biochemistry Laboratory
- 2002
- Lecturer, Institute of Molecular and Cellular Biosciences, The University of Tokyo
- 1998
- Research Associate, Institute for Molecular Science
- 1998
- Ph. D (Chemistry), Graduate School of Science, Kyoto University
Keyword
- Molecular Dynamics
- Protein Dynamics
- Free Energy Calculation
- Machine Learning
- Parallelization
Research summary
To understand a wide variety of biological processes in cells, it is often necessary to evaluate their underlying free-energy changes with great accuracy. Protein folding and unfolding, receptor-drug interactions, protein-protein and protein-DNA associations are such examples. Our research team aims to develop efficient and accurate methodologies for free-energy calculations for biological systems. We are developing novel algorithms coupled with different molecular models such as coarse-grained, all-atom, and hybrid QM/MM models. We also optimize our software to the supercomputer Fugaku, the world-fastest supercomputer developed at RIKEN R-CCS. The method and software we have developed will be provided to researchers in the fields of computational biophysics and computer-aided rational drug design.
Main research results
Representative papers
- Yu, I., Mori, T., Ando, T., Harada, R., Jung, J., Sugita, Y., and Feig, M.:
"Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm"
eLife, 5, e19274 (2016). - Jung, J., Naruse, A., Kobayashi, C., and Sugita, Y.:
"Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations"
J. Chem. Theory Comput. 12, 4947-4958 (2016). - Matsunaga, Y., Komuro, Y., Kobayashi, C., Jung, J., Mori, T., and Sugita, Y.:
"Dimensionality of Collective Variables for Describing Conformational Changes of a Multi-Domain Protein"
J. Phys. Chem. Lett. 7, 1446-1451 (2016). - Kobayashi, C., Matsunaga, Y., Koike R., Ota M., and Sugita Y.:
"Domain Motion Enhanced (DoME) Model for Efficient Conformational Sampling of Multidomain Proteins"
J. Phys. Chem. B 119, 14584-14593 (2015). - Jung J., Kobayashi C., Imamura T., and Sugita Y.:
"Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations"
Comp. Phys. Comm 200, 57-65 (2015). - Fujisaki H., Moritsugu K., Matsunaga Y., Morishita T., and Maragliano L.:
"Extended phase-space methods for enhanced sampling in molecular simulations: a review"
Front. Bioeng. Biotechnol. (2015). doi: 10.3389/fbioe.2015.00125 - Matsunaga Y., Kidera A., and Sugita Y.:
"Sequential data assimilation for single-molecule FRET photon-counting data"
J. Chem. Phys. 142, 214115 (2015). - Galvelis R., and Sugita Y.:
"Replica State Exchange Metadynamics for Improving the Convergence of Free Energy Estimates"
J. Comp. Chem. 36, 1446-1455 (2015). - Jung J., Mori T., Kobayashi C., Matsunaga Y., Yoda T., Feig M., and Sugita Y.:
"GENESIS: A hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations"
WIREs Comp. Mol. Sci. 5, 310-323 (2015). - Feig M., Harada R., Mori T., Yu I., Takahashi K., and Sugita Y.:
"Complete Atomistic Model of a Bacterial Cytoplasm for Integrating Physics Biochemistry, and Systems Biology"
J. Mol. Graph. Modeling 58, 1-9 (2015).
Annual Reports
Press Releases & Other News
- Glycans are crucial in COVID-19 infection (Mar 24, 2021, RIKEN Website)
Members
Related Websites
Molecular dynamics simulation software GENESIS
Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research (CPR)
Laboratory of Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research (BDR)
Feig Lab, Department of Biochemistry and Molecular Biology, Michigan State University (Prof. Michael Feig)
Graduate School of Life Science, University of Hyogo (Prof. Yoshitsugu Shiro)