The aim of this laboratory is structural bioinformatics covering molecular modeling and design of proteins and other biological macromolecules: Development of a new database, eF-site, for protein surface geometry with the physicochemical properties, and identification of protein functions using the database, and Development of new algorithms and softwares for large scale simulation calculations by parallel computers to examine free energy landscapes of biomolecular systems. A new hybrid method of Quantum Mechanics and Molecular Mechanics has also been developed for analysis of the electronic state in biological macromolecular systems.

Publication List:

Kinoshita, K., Nakamura, H. (2003) Protein informatics towards function identification. Curr. Opin. Struct. Biol. 13, 396-400.

Kinoshita, K., Nakamura, H. (2003) Identification of protein biochemical functions by similarity search using the molecular surface database, eF-site. Protein Science, 12, 1589-1595.

Kim, J. G., Fukunishi, Y., Kidera, A., Nakamura, H. (2003) Determination of multicanonical weight based on stochastic model of sampling dynamics. Phys. Rev. E 68, 21110.

Fukunishi, Y., Mikami, Y., Nakamura, H. (2003) The filling potential method: a method for estimating the free energy surface for protein-ligand docking. J. Phys. Chem. B, 107, 13201-13210.

Fukuda, I., Nakamura, H. (2003) Deterministic generation of the Boltzmann-Gibbs distribution and the free energy calculation form the Tsallis distribution. Chem. Phys. Lett. 382, 367-373.