Annual Report 2002
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DIVISION OF BIOINFORMATICS

Professor (Adjunct): NAKAMURA, Haruki (Osaka University)

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.

Publication list:

Fukuda, I. and Nakamura, H. (2002) Tsallis Dynamics Using the Nose-Hoover Approach. Physical Review E., 65, 26105.

Kamiya, N., Higo, J., Nakamura, H. (2002) Conformational Transition States of Beta-hairpin Peptide between the Ordered and Disordered Conformations in Explicit Water. Protein Science, 11, 2297-2307.

Ono, S., Kuroda, M., Higo, J., Nakajima, N., and Nakamura, H. (2002) Calibration of Force Field Dependency in Free Energy Landscapes of Peptide Conformations by Quantum Chemical Calculations. Journal of Computational Chemistry, 23, 470-476.

Tsuchiya, Y., Kinoshita, K., and Nakamura ,H. (2002) Analysis of Complementarity of Protein-DNA Interactions Using the Electrostatic Potential and the Molecular Surface Geometry. Genome Informatics, 13, 310-311.


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