Computational Biology Research Center[CBRC]

Research Topics

■ Development of complex structure calculation technology

Calculate protein-protein docking using high-throughput numerical libraries and research on, protein-carbohydrate chain interactions by large-scale parallel computer processing.

■ Development of functional prediction technology

Enable the prediction of the structures (RNA) and functional sites based on protein-complex structure, and ultimately the prediction of protein function through the integration of calculation and network dynamical analysis.

■ Establishment of applied large-scale calculation technology platform

Develop fundamental technologies that will provide a foundation to support drug discovery and biological polymer regulation (intermolecular interaction) research, based in store of quantum chemistry, molecular dynamics, and molecular docking computational technologies that have been developed to date.

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Team Member

Kazuhiko Fukui

Leader E-mail

website

Key Words

Molecular Simulation, Saccharides, GRID, HPC, Protein Interaction, Fragmentation Mechanism, LASER, Photo-induced reaction

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Atsushi Suenaga

Invited Senior
Research Scientist

website

E-mail

Key Words

molecular simulation, protein-protein interaction, Free energy calculation, molecular design

Daisuke Tominaga

Research
Scientist

website

E-mail

Key Words

Systems biology, Time series analysis, Symbolic computation, Numerical optimization, Gene regulatory networks, S-system, Periodicity judgment

Satoshi Yamasaki

AIST
Research Staff

website

E-mail

Key Words

Protein - DNA/RNA interaction, DNA/RNA folding, molecular dynamics simulation

Papers List

• ■ S. Yamasaki, S. Nakamura, K. Fukui, "Prospects for tertiary structure prediction of RNA based on secondary structure information." Journal of Chemical Information and Modeling, 52, pp.557-567 (2012).
• ■ K. Fukui, K. Takahashi, "Infrared multiple photon dissociation Spectroscopy and Computational Studies of O-Glycosylated Peptides." Analytical Chemistry, 84, pp.2188-2194 (2012).
• ■ M. M. Gromiha, N. Saranya, S. Selvaraj, B. Jayaram, K. Fukui, "Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes." Proteome Science, 9:S13 (2011).
• ■ M. M. Gromiha, K. Fukui, "Scoring Function Based Approach for Locating Binding Sites and Understanding Recognition Mechanism of Protein-DNA Complexes." Journal of Chemical Information and Modeling, 51, pp.721-729 (2011).
• ■ W. Nemoto, K. Fukui, H. Toh, "GRIPDB - G protein coupled Receptor Interaction Partners DataBase." Journal of Receptors and Signal Transduction, 31, pp.199-205 (2011).
• ■ D. Tominaga, "Periodicity detection method for small-sample time series datasets", Bioinformatics and Biology Insights, 4, pp.127-136 (2010).