Centers & Labs

RIKEN Quantitative Biology Center

Drug Discovery Molecular Simulation Platform Unit

Unit Leader: Makoto Taiji (D. Sci.)
Makoto  Taiji(D. Sci.)

This unit aims to use leading computational technologies using large-scale, high-speed supercomputers for in silico drug discovery. In particular, we are focusing on molecular simulation technologies to predict high-precision binding affinity, taking into account the dynamics of complex structures consisting of proteins and other low molecular compounds while in aqueous solution for better estimations on binding affinities and other drug efficacy parameters. Such studies will help identify drug behavior at the molecular level and help predict what structural formulas make for highly effective and selective drug candidates.

Main Research Field

Informatics

Related Research Fields

Medicine, dentistry, and pharmacy

Keywords

  • Computational Drug Design
  • Computational Chemistry
  • High-Performance Computing
  • Special-purpose computer
  • Molecular Dynamics simulations

Selected Publications

  1. Noriaki Okimoto, Atsushi Suenaga and Makoto Taiji:
    "Evaluation of protein–ligand affinity prediction using steered molecular dynamics simulations."
    Journal of Biomolecular Structure and Dynamics. Nov.7, pp.1-11 (2016)
  2. Junya Yamagishi, Noriaki Okimoto, Gentaro Morimoto and Makoto Taiji:
    "A New set of atomic Radii for Accurate Estimation of Solvation Free Energy by Poisson-Boltzmann Solvent Model."
    Journal of Computational Chemistry. Vol.35, Issue.29, pp.2132-2139 (2014)
  3. Hiroko X. Kondo, Noriaki Okimoto, Gentaro Morimoto, and Makoto Taiji:
    "Free-Energy Landscapes of Protein Domain Movements upon Ligand Bindin."
    J. Phys. Chem. Vol.115, No.23, pp.7629-7636 (2011)
  4. Noriaki Okimoto, Noriyuki Futatsugi, Hideyoshi Fuji1,3, Atsushi Suenaga, Gentaro Morimoto, Ryoko Yanai, Yousuke Ohno, Tetsu Narumi, and Makoto Taiji:
    "High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations."
    PLoS Comput Biol Vol.5(10): e1000528. doi:10.1371/journal.pcbi.1000528 (2009)
  5. Atsushi Suenaga, Naoki Takada, Mariko Hatakeyama, Mio Ichikawa, Xiaomei Yu, Kentaro Tomii, Noriaki Okimoto, Noriyuki Futatsugi, Tetsu Narumi, Mikako Shirouzu, Shigeyuki Yokoyama, Akihiko Konagaya, and Makoto Taiji:
    "Novel Mechanism of Interaction of p85 Subunit of Phosphatidylinositol 3-Kinase and ErbB3 Receptor-derived Phosphotyrosyl Peptides."
    THE JOURNAL OF BIOLOGICAL CHEMISTRY 280, pp.1321-1326 (2005)
  6. Atsushi Suenaga, Mariko Hatakeyama, Mio Ichikawa, Xiaomei Yu, Noriyuki Futatsugi, Tetsu Narumi,Kazuhiko Fukui, Takaho Terada, Makoto Taiji, Mikako Shirouzu, Shigeyuki Yokoyama, and Akihiko Konagaya:
    "Molecular Dynamics, Free Energy, and SPR Analyses of the Interactions between the SH2 Domain of Grb2 and ErbB Phosphotyrosyl Peptides."
    Biochemistry Vol.42, pp.5195-5200 (2003)

Lab Members

Principal Investigator

Makoto Taiji
Unit Leader

Core Members

Noriaki Okimoto
Senior Scientist
Shigeo Fujita
Senior Scientist
Yoshinori Hirano
Research Scientist
Gentaro Morimoto
Technical Scientist

Contact information

2F, QBiC Building B,
6-2-4, Furuedai
Suita, Osaka
565-0874 JAPAN

Email: taiji [at] riken.jp

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