Computational Biophysics Research Team

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.

Research Subjects

• 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

Publications

1. Y. Matsunaga, H. Fujisaki, T. Terada, T. Furuta, K. Moritsugu, and A. Kidera:
   "Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase"
   PLoS Comput. Biol. 8 (2012) e1002555
2. R. Harada, Y. Sugita, and M. Feig:
   "Protein Crowding Affects Hydration Structure and Dynamics"
   J. Am. Chem. Soc. 134 (2012) 4842-4849
3. S. Re, T. Imai, J. Jung, S. Ten-no, and Y. Sugita:
   "Geometrically Associate Yet Electronically Dissociative Character in the Transition State of Enzymatic Reversible Phosphorylation"
   J. Comput. Chem. 32 (2011) 260-270
4. 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