Centers & Labs

RIKEN Center for Computational Science

Computational Biophysics Research Team

Team Leader: Yuji Sugita (D.Sci.)
Yuji  Sugita(D.Sci.)

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 K computer, the world-fastest supercomputer developed at RIKEN AICS. 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 Field

Chemistry

Related Research Fields

Complex systems / Mathematical and physical sciences / Biological Sciences

Keywords

  • Molecular Dynamics
  • Protein Dynamics
  • Free Energy Calculation
  • Machine Learning
  • Parallelization

Selected Publications

  1. 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).
  2. 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).
  3. 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).
  4. 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).
  5. 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).
  6. 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
  7. Matsunaga Y., Kidera A., and Sugita Y.:
    "Sequential data assimilation for single-molecule FRET photon-counting data"
    J. Chem. Phys. 142, 214115 (2015).
  8. Galvelis R., and Sugita Y.:
    "Replica State Exchange Metadynamics for Improving the Convergence of Free Energy Estimates"
    J. Comp. Chem. 36, 1446-1455 (2015).
  9. 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).
  10. 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).

Lab Members

Principal Investigator

Yuji Sugita
Team Leader

Core Members

Osamu Miyashita
Senior Scientist
Suyong Re
Research Scientist
Kiyoshi Yagi
Research Scientist
Yasuhiro Matsunaga
Research Scientist
Takaharu Mori
Research Scientist
Jaewoon Jung
Research Scientist
Chigusa Iwahashi
Research Scientist
Isseki Yu
Research Scientist
Ai Niitsu
Special Postdoctoral Researcher
Motoshi Kamiya
Postdoctoral Researcher
Koichi Tamura
Postdoctoral Researcher
Hiraku Oshima
Postdoctoral Researcher
Mitsunori Ikeguchi
Visiting Scientist
Naoyuki Miyashita
Visiting Scientist
Takao Yoda
Visiting Scientist
Michael Feig
Visiting Scientist

Contact information

Integrated Innovation Building 7F,
6-7-1 Minatojima-minamimachi,
Chuo-ku,Kobe,Hyogo
650-0047,Japan

Email: sugita [at] riken.jp

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