Computational Biophysics Research Team
Team Leader
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.
- Development of multi-scale/multi-resolution methods
- Development of the generalized-ensemble algorithms and their applications to biomolecules
- Improvement of hybrid QM/MM calculations
- Parallelization of molecular dynamics simulation software and its optimization to K computer
- S. Re, T. Imai, J. Jung, S. Ten-no, and Y. Sugita,:
"Geometrically Associative Yet Electronically Dissociative Character in the Transition State of Enzymatic Reversible Phosphorylation"
J. Comp. Chem. 32 (2011) 260-270. - J. Jung, Y. Sugita, and S. Ten-no,:
"Moller-Presset perturbation theory gradient in the generalized hybrid orbital quantum mechanical and molecular mechanical method"
J. Chem. Phys. 132 (2010) 084106. - S. Re, J. Jung, S. Ten-no, and Y. Sugita,:
"A two-dimensional energy surface of the phosphoryl transfer reaction catalyzed by phosphoserine phophatase"
Chem. Phys. Lett. 480 (2009) 284-288. - J. Jung, C.H. Choi, Y. Sugita, and S. Ten-no,:
"New implementation of a combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals"
J. Chem. Phys. 127 (2007) 204102.
Principal Investigator
- Yuji SUGITA
- Team Leader
Staff Scientist
- Jaewoon JUNG
- Research Scientist
Postdoctoral Fellow
- Yasuhiro MATSUNAGA
- Special Postdoctoral Researcher
- Ryuhei HARADA
- Postdoctoral Researcher
- Raimondas GALVELIS
- Postdoctoral Researcher
Visiting Research Staff
- Mitsunori IKEGUCHI
- Visiting Scientist
- Takao YODA
- Visiting Scientist