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Laboratory for Computational Molecular Design

Makoto Taiji


Group Director

Makoto Taiji (D.Sci.)

Taiji of Riken

The Computational Molecular Design Group aims to simulate biomolecular interactions and to design effective molecular regulators using large-scale computer simulations. X-ray crystallography and NMR studies provide a large number of 3D structures of biomolecules, and advances in molecular detection technologies have greatly improved our understandings of intracellular molecular behaviors. To connect molecular behavior with molecular structure and to predict molecular functions, however, require large scale, atomic level molecular simulations. We are therefore focusing on molecular dynamics (MD) and quantum chemistry simulations to study this relationship in large biomolecules. Through collaboration with groups inside and outside QBiC, we are designing novel compounds for various target biomolecules by utilizing our computational techniques. Furthermore, by developing exclusive high-performance computers, we aim to achieve unprecedented long-term MD simulations.

Research Topics

  • Understanding thermodynamic and physicochemical properties of the interaction of biopolymers with their regulators and hydration water
  • Theoretical study on binding and enzymatic reactions of protein/DNA-regulator complexes
  • Designing new peptides for protein target binding
  • Development of MDGRAPE-4, a special purpose computer for MD simulations.

Selected Publications

  • Otsuka, T., Okimoto, N. & Taiji, M.
    "Assessment and acceleration of binding energy calculations for protein-ligand complexes by the fragment molecular orbital method"
    J. Comput. Chem. 36, 2209-2218 (2015)
  • Yamagishi, J., Okimoto, N., Morimoto, G. & Taiji, M.
    "A New Set of Atomic Radii for Accurate Estimation of Solvation Free Energy by Poisson-Boltzmann Solvent Model"
    J. Comput. Chem. 35, 2132-2139 (2014) doi:10.1002/jcc.23728
  • Ohno, Y., Yokota, R., Koyama, H., Morimoto, G., Hasegawa, A., Masumoto, G., et al.
    "Petascale molecular dynamics simulation using the fast multipole method on K computer"
    Comput. Phys. Commun. 185, 2575-2585 (2014) doi:10.1016/j.cpc.2014.06.004
  • Ohmura, I., Morimoto, G., Ohno, Y., Hasegawa, A. & Taiji, M.
    "MDGRAPE-4: a special-purpose computer system formolecular dynamics simulations"
    Philosophical Transactions of the Royal Society a-Mathematical Physical and Engineering Sciences 372, 20130387 (2014) doi:10.1098/rsta.2013.0387
  • Kondo, H. X. & Taiji, M.
    "Enhanced exchange algorithm without detailed balance condition for replica exchange method"
    J. Chem. Phys. 138, 244113 (2013) doi:10.1063/1.4811711
  • Kondo, H. X., Okimoto, N., Morimoto, G. & Taiji, M.
    "Free-Energy Landscapes of Protein Domain Movements upon Ligand Binding"
    J. Phys. Chem. B 115, 7629-7636 (2011) doi:10.1021/jp111902t
  • Hamada, T., Narumi, T., Yokota, R., Yasuoka, K., Nitadori, K. & Taiji, M.
    "42 TFlops hierarchical N-body simulations on GPUs with applications in both astrophysics and turbulence"
    Proc. Supercomputing 2009 , 62 (2009) doi:10.1145/1654059.1654123
  • Okimoto, N., Futatsugi, N., Fuji, H., Suenaga, A., Morimoto, G., Yanai, R., et al.
    "High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations"
    PLoS Comput. Biol. 5, e1000528 (2009) doi:10.1371/journal.pcbi.1000528
  • Ohno, Y., Nishibori, E., Narumi, T., Koishi, T., Tahirov, T. H., Ago, H., et al.
    "A 281 Tflops Calculation for X-ray Protein Structure Analysis with Special-Purpose Computers MDGRAPE-3 "
    In Proceedings of the SC07. (2007)
  • Narumi, T., Ohno, Y., Okimoto, N., Koishi, T., Suenaga, A., Futatsugi, N., et al.
    "A 55 TFLOPS Simulation of Amyloid-forming Peptides from Yeast Prion Sup35 with the Special-purpose Computer System MDGRAPE-3"
    In Proceedings of the SC06. (2006)