Laboratory for Computational Molecular Design | RIKEN BDR

Laboratory for Computational Molecular Design

Team Leader

Makoto TaijiD.Sci.

Photo of principal investigator

  • Location:Osaka / Quantitative Biology Buildings
  • E-mail:taiji[at]riken.jpPlease replace [at] with @.

Research Summary

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 BDR, 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 Theme

Main Publications List

  • Komatsu TS, Okimoto N, Koyama YM, et al.
    Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation
    Scientific Reports 10. 16986 (2020) doi: 10.1038/s41598-020-74099-5
  • COVID-19 related trajectory data of 10 microseconds all atom molecular dynamics simulation of SARS-CoV-2 dimeric main protease
    Mendeley Data, 10.17632/vpps4vhryg.1
    doi: 10.17632/vpps4vhryg.1
  • Takaoka Y, Iwahashi M, Chini A, et al.
    A rationally designed JAZ subtype-selective agonist of jasmonate perception.
    Nature Communications 9. 3654 (2018) doi: 10.1038/s41467-018-06135-y
  • Otsuka T, Okimoto N, Taiji M.
    Assessment and acceleration of binding energy calculations for protein-ligand complexes by the fragment molecular orbital method.
    Journal of Computational Chemistry 36(30). 2209-2218 (2015) doi: 10.1002/jcc.24055
  • 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.
    Journal of Computational Chemistry 35(29). 2132-2139 (2014) doi: 10.1002/jcc.23728
  • Ohno Y, Yokota R, Koyama H, et al.
    Petascale molecular dynamics simulation using the fast multipole method on K computer.
    Computer Physics Communications 185(10). 2575-2585 (2014) doi: 10.1016/j.cpc.2014.06.004
  • Ohmura I, Morimoto G, Ohno Y, et al.
    MDGRAPE-4: a special-purpose computer system formolecular dynamics simulations.
    Philosophical Transactions of the Royal Society a-Mathematical Physical and Engineering Sciences 372(2021). 20130387 (2014) doi: 10.1098/rsta.2013.0387
  • Kondo HX, Taiji M.
    Enhanced exchange algorithm without detailed balance condition for replica exchange method.
    Journal of Chemical Physics 138(24). 244113 (2013) doi: 10.1063/1.4811711
  • Kondo HX, Okimoto N, Morimoto G, Taiji M.
    Free-Energy Landscapes of Protein Domain Movements upon Ligand Binding.
    Journal of Physical Chemistry B 115(23). 7629-7636 (2011) doi: 10.1021/jp111902t
  • Hamada T, Narumi T, Yokota R, et al.
    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, et al.
    High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations.
    Plos Computational Biology 5(10). e1000528 (2009) doi: 10.1371/journal.pcbi.1000528
  • Ohno Y, Nishibori E, Narumi T, et al.
    A 281 Tflops Calculation for X-ray Protein Structure Analysis with Special-Purpose Computers MDGRAPE-3.
    In Proceedings of the SC07 (2007) doi: 10.1145/1362622.1362698
  • Narumi T, Ohno Y, Okimoto 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) doi: 10.1145/1188455.1188506