RIKEN Center for Computational Science Life and Medical Science Application Interface Platform Development Unit
Unit Leader: Yuji Sugita (D.Sc.)
Research Summary
The structure and dynamics of biomacromolecules are not only crucial for maintaining life activities but are also related to diseases, making their detailed observation important. We are developing AI-based technologies to combine image data obtained from advanced experimental methods such as High-Speed AFM, Cryo-EM/ET, and state-of-the-art microscopy techniques with the three-dimensional structures of biomacromolecules. Additionally, we are developing application interfaces and workflow technologies to integrate measurement data with molecular structures and dynamics. Furthermore, we are developing an application interface platform to connect software developed for scientific research using high-performance computing with AI.
Main Research Fields
- Biological Sciences
Related Research Fields
- Chemistry
- Complex Systems
Selected Publications
- 1.
J. Jung, K. Yagi, C. Tan, H. Oshima, T. Mori, I.Yu, Y. Matsunaga,C. Kobayashi, S. Ito, D. Ugarte La Torre, Y. Sugita
"GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and
Free-Energy Calculations for Atomistic, Coarse-Grained, and QM/MM models",
J. Phys. Chem. B. (2024) in press. - 2.
J. Jung, C. Tan, Y. Sugita
"GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems",
Nature Comm. 15, 3370 (2024). - 3.
C. Tan, J. Jung, C. Kobayashi, D. Ugarte, S. Takada, Y. Sugita
"Implementation of residue-level coarse-grained models I GENESIS for large-scale molecular dynamics simulations",
PLoS Comp. Biol. 18, e1009578 (2022). - 4.
"Y. Matsunaga, M. Kamiya, H. Oshima, J. Jung, S. Ito, and Y. Sugia*
"Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation",
Biophysical Reviews 14, 1503-1512 (2022). - 5.
Y. Matsunaga, and Y. Sugita*
"Use of single-molecule time-series data for refining conformational dynamics in molecular simulations",
Current Opinion in Structural Biology 61, 153-159 (2020). - 6.
Y. Matsunaga, and Y. Sugita*,
"Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning",
eLife 7, e32668 (2018). - 7.
Y. Matsunaga, and Y. Sugita*,
"Refining Markov State Models for conformational dynamics using ensemble-averaged data and time-series trajectories",
The Journal of Chemical Physics 148, 241731 (2018).
Lab Members
Principal investigator
- Yuji Sugita
- Unit Leader
Core members
- Osamu Miyashita
- Senior Scientist
- Cheng Tan
- Research Scientist
- Diego Renato Ugarte La Torre
- Postdoctoral Researcher
- Tingting Wang
- Postdoctoral Researcher
- Yasuhiro Matsunaga
- Visiting Scientist
Contact Information
Integrated Innovation Building (IIB)
6-7-1 Minatojima-minamimachi,
Chuo-ku, Kobe,Hyogo
650-0047, Japan
Email: sugita [at] riken.jp