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Exploring the scientific foundations of life through interdisciplinary approaches to address society’s problems.

Photo of Unit leder, Makoto Taiji

Unit Leader
Makoto Taiji D.Sci.

Drug Discovery Molecular Simulation Platform Unit

Location Osaka / Quantitative Biology Buildings

E-mail taiji[at]riken.jp

Please replace [at] with @.

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.

Research Theme

  • Large-scale, high-speed super computing for in silico drug discovery
  • In silico screening of drug compounds for protein targets
  • Developing of high affinity compounds based on the simulations from (2)

Selected Publications

Okimoto N, Suenaga A, Taiji M.
Evaluation of protein–ligand affinity prediction using steered molecular dynamics simulations.
Journal of Biomolecular Structure and Dynamics 35(15), 1-11 Thu Dec 01 00:00:00 JST 2016 doi: 10.1080/07391102.2016.1251851

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 Mon Dec 01 00:00:00 JST 2014 doi: 10.1002/jcc.23728

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 Thu Dec 01 00:00:00 JST 2011 doi: 10.1021/jp111902t

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 Tue Dec 01 00:00:00 JST 2009 doi: 10.1371/journal.pcbi.1000528

Suenaga A, Takada N, Hatakeyama M, et al.
Novel mechanism of interaction of p85 subunit of phosphatidylinositol 3-kinase and ErbB3 receptor-derived phosphotyrosyl peptides.
Journal of Biological Chemistry 280(2), 1321-1326 Thu Dec 01 00:00:00 JST 2005 doi: 10.1074/jbc.M410436200

Suenaga A, Hatakeyama M, Ichikawa M, et al.
Molecular dynamics, free energy, and SPR analyses of the interactions between the SH2 domain of grb2 and ErbB phosphotyrosyl peptides.
Biochemistry 42(18), 5195-5200 Mon Dec 01 00:00:00 JST 2003 doi: 10.1021/bi034113h

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