RIKEN Center for Computational Science Computational Biophysics Research Team

Team Leader: Yuji Sugita (D.Sc.)

Japanese Page

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 suprecomputer 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 Fields

Chemistry

Related Research Fields

Complex Systems
Mathematical & 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).