Computational Biology Research Center[CBRC]

Advanced Industrial Science and Technology[AIST]
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Molecular Function Team

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.


¢£click for full size(219KB)

Team Member

Kazuhiko Fukui
Leader E-mail
Kazuhiko Fukui
Key Words

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


Atsushi Suenaga
Invited Senior
Research Scientist
E-mail
Key Words

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


Daisuke Tominaga
Research
Scientist
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
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).
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