Computational Biology Research Center[CBRC]
Advanced Industrial Science and Technology[AIST]- Genome
Informatics - RNA Informatics
- Sequence Analysis
- Molecular Informatics
- Molecular Modeling & Drug Design
- Molecular Function
- Cellar
Informatics - Cell Function Design
- Biological Network
- Top
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- Organization
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- Molecular Function Team
Molecular Function Team
The Molecular Function Team seeks to develop technologies for the computation of the properties of complexes formed by proteins with proteins or other biological molecules (compound, carbohydrate chain, etc.), and the prediction of biological polymer function based on predicted structure, primarily for applications in large-scale computation. Inspired by the technological developments that have driven bioinformatics research using the world’s most powerful parallel computers, such as the Magi cluster, AIST super cluster, and BlueProtein system, we are working toward developing applications by making effective use of large-scale parallel computing. We seek to:
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 super parallel computer processing.
■Development of functional prediction technology
Enable the prediction of the structures of functional sites by flexible site prediction based on changes in protein structure, and ultimately of protein function through the integration of docking calculation to promote the efficiency of drug development.
■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.
Team Member
Kazuhiko Fukui
Key Words
Molecular Simulation, Saccharides, Glyco-peptide/protein, Mass Spectrometry, Fragmentation Mechanism, LASER, Photo-induced reaction
Michael Gromiha
Research
Scientist
Key Words
Membrane and Globular Proteins、structural analysis、discrimination、prediction、folding、stability、protein-DNA interactions、database、statistical methods、machine learning techniques
Wataru Nemoto
Research Staff
Key Words
Functional analysis, sequence and structure information, prediction of functional regions, prediction of interfaces, protein-protein interaction, drug design, globular and membrane proteins, GPCRs
Satoshi Yamasaki
Research Staff
Key Words
Protein - DNA/RNA interaction, DNA/RNA folding, molecular dynamics simulation
Papers List
- ■ Tsukamoto K (Tsukamoto, Koki), Shimizu H (Shimizu, Hideaki), Ishida T (Ishida, Takashi), Akiyama Y (Akiyama, Yutaka), Nukina N (Nukina, Nobuyuki) "Evaluation for interaction energy between glutamine and various chemical compounds for developing the virtual screening system using DFT quantum chemical calculations", WSEAS TRANSACTIONS ON COMPUTERS 6, 636-641 (2007).
- ■ Gromiha, M.M., Thangakani, A.M., Selvara,j S.: "FOLD-RATE: prediction of protein folding rates from amino acid sequence", Nucleic Acids Research, 34(Web Server issue), pp.W70-W74 (2006).
- ■ Tsukamoto K (Tsukamoto, Koki), Shimizu H (Shimizu, Hideaki), Ishida T (Ishida, Takashi), Akiyama Y (Akiyama, Yutaka), Nukina N (Nukina, Nobuyuki) "Aggregation mechanism of polyglutamine diseases revealed using quantum chemical calculations, fragment molecular orbital calculations, molecular dynamics simulations, and binding free energy calculations", JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM 778 (1-3): 85-95 (2006).
- ■ Gromiha, M.M., Selvaraj, S., Thangakani A.M.: "A statistical method for predicting protein unfolding rates from amino acid sequence", Journal of Chemical Information and Modeling, 46 (3), pp.1503 - 1508 (2006).
- ■ Fukui, K., Kameyama, A., Mukai, Y., Takahashi, K., Ikeda, N., Akiyama, Y., Narimatsu, H.: "A computational study of structure-reactivity relationships in Na-adduct oligosaccharides in collision-induced dissociation reactions", Carbohydrate Research, 341(5), pp.624-633 (2006).