M. Taiji

发表

Nanoscale elongating control of the self‐assembled protein filament with the cysteine‐introduced building blocks

Y. Hayashizaki, Harukazu Suzuki, M. Itoh, 2009, Protein science : a publication of the Protein Society.

Structure and dynamics of RNA polymerase II elongation complex.

Toshikazu Ebisuzaki, Akihiko Konagaya, Makoto Taiji, 2006, Biochemical and biophysical research communications.

Title Molecular Dynamics Simulations Reveal that Tyr-317 Phosphorylation Reduces Shc Binding Affinity for Phosphotyrosyl Residues of Epidermal Growth Factor Receptor

B. Kholodenko, A. Kiyatkin, M. Hatakeyama, 2017 .

Molecular dynamics simulations reveal that Tyr-317 phosphorylation reduces Shc binding affinity for phosphotyrosyl residues of epidermal growth factor receptor.

B. Kholodenko, A. Kiyatkin, M. Hatakeyama, 2009, Biophysical journal.

Folding Dynamics of 10‐Residue β‐Hairpin Peptide Chignolin

Makoto Taiji, Noriaki Okimoto, Noriyuki Futatsugi, 2007 .

GRAPE-4: A Massively Parallel Special-Purpose Computer for Collisional N-Body Simulations

Toshikazu Ebisuzaki, Makoto Taiji, Junichiro Makino, 1997 .

Structural and Functional Basis of a Role for CRKL in a Fibroblast Growth Factor 8-Induced Feed-Forward Loop

M. Hatakeyama, A. Suenaga, M. Taiji, 2009, Molecular and Cellular Biology.

Enhanced exchange algorithm without detailed balance condition for replica exchange method.

M. Taiji, Hiroko X. Kondo, 2013, The Journal of chemical physics.

Molecular phase space transport in water: non-stationary random walk model

M. Taiji, D. Nerukh, V. Ryabov, 2009 .

Structural characteristics of hydration sites in lysozyme.

M. Taiji, K. Soda, Yudai Shimbo, 2011, Biophysical chemistry.

Linear-scaling first-principles molecular dynamics of complex biological systems with the Conquest code

D. Bowler, T. Miyazaki, M. Taiji, 2016 .

HARP--A Special-Purpose Computer for N-Body Problem (GRAPE)

J. Makino, E. Kokubo, M. Taiji, 1993 .

Special-Purpose Computers for Classical Particle Simulations

M. Taiji, 2001 .

Ligand Di ff usion on Protein Surface Observed in Molecular Dynamics Simulation

A. Suenaga, M. Taiji, N. Okimoto, 2012 .

FEMTOSECOND STUDIES OF PRIMARY PHOTOPROCESSES IN OCTOPUS RHODOPSIN

Takayoshi Kobayashi, M. Taiji, K. Bryl, 1992 .

Femtosecond spectroscopy of acidified and neutral bacteriorhodopsin

Makoto Taiji, Takayoshi Kobayashi, Mamoru Terauchi, 1991, Other Conferences.

Femtosecond Spectroscopy of Halorhodopsin and Rhodopsin in a Broad Spectral Range of 400−1000 nm

Takayoshi Kobayashi, M. Taiji, M. Nakagawa, 1998 .

All-atom molecular dynamics analysis of multi-peptide systems reproduces peptide solubility in line with experimental observations

A. Suenaga, M. Taiji, Y. Kuroda, 2016, Scientific Reports.

Accurate Estimation of the Dynamical Critical Exponent of the Two-Dimensional Kinetic Ising Model Based on the Ising Machine m-TIS

Makoto Taiji, Nobuyasu Ito, M. Suzuki, 1987 .

Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation

Yohei M. Koyama, M. Taiji, Y. Hirano, 2020, Scientific reports.

Use of the Multilayer Fragment Molecular Orbital Method to Predict the Rank Order of Protein–Ligand Binding Affinities: A Case Study Using Tankyrase 2 Inhibitors

M. Taiji, Y. Hirano, N. Okimoto, 2018, ACS omega.

Single-molecule motions of MHC class II rely on bound peptides.

M. Taiji, N. Okimoto, K. Ichiyanagi, 2015, Biophysical journal.

Transacylation rates of (aminoacyl)adenosine moiety at the 3'-terminus of aminoacyl transfer ribonucleic acid.

S. Yokoyama, M. Taiji, T. Miyazawa, 1983, Biochemistry.

Reversible hydrogel formation driven by protein-peptide-specific interaction and chondrocyte entrapment.

Y. Hayashizaki, Harukazu Suzuki, M. Itoh, 2010, Biomaterials.

A leukotriene C4 synthase inhibitor with the backbone of 5-(5-methylene-4-oxo-4,5-dihydrothiazol-2-ylamino) isophthalic acid.

M. Taiji, N. Okimoto, Y. Kanaoka, 2013, Journal of biochemistry.

Ultrafast nonlinear processes in one-dimensional J-aggregates

K. Misawa, K. Minoshima, M. Taiji, 1994, Proceedings of 1994 Nonlinear Optics: Materials, Fundamentals and Applications.

Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation

Yohei M. Koyama, M. Taiji, Y. Hirano, 2020, Scientific Reports.

Application of order-N first-principles DFT calculations with temperature controlled molecular dynamics to biomolecular system

M. Taiji, T. Otsuka, 2018, Journal of Physics: Conference Series.

Slow transacylation of peptidyladenosine allows analysis of the 2'/3'-isomer specificity of peptidyltransferase.

S. Yokoyama, M. Taiji, T. Miyazawa, 1985, Biochemistry.

Crystal Structure of the Rac Activator, Asef, Reveals Its Autoinhibitory Mechanism*

Y. Kawasaki, T. Akiyama, S. Yokoyama, 2007, Journal of Biological Chemistry.

Femtosecond Spectroscopy of Poly(3-Methylthiophene) Films

Takayoshi Kobayashi, K. Yoshino, M. Taiji, 1990 .

Large-scale all-atom molecular dynamics alanine-scanning of IAPP octapeptides provides insights into the molecular determinants of amyloidogenicity

M. Taiji, Y. Kuroda, Richa Tambi, 2019, Scientific Reports.

In vitro selection of a peptide aptamer that potentiates inhibition of cyclin-dependent kinase 2 by purvalanol

Yoshihiro Ito, M. Taiji, Y. Hirano, 2014 .

AdamB: Decoupled Bayes by Backprop With Gaussian Scale Mixture Prior

M. Taiji, Keigo Nishida, 2022, IEEE Access.

Dynamics of internal models in game players

Makoto Taiji, Takashi Ikegami, T. Ikegami, 1998, adap-org/9807004.

Two Novel ALK Mutations Mediate Acquired Resistance to the Next-Generation ALK Inhibitor Alectinib

A. Iafrate, J. Engelman, Y. Okuno, 2014, Clinical Cancer Research.

Femtosecond nonlinear optical dynamics of excitons in J-aggregates

Makoto Taiji, Kaoru Minoshima, Kazuhiko Misawa, 1994 .

Dynamic interactions of cations, water and lipids and influence on membrane fluidity

M. Yasui, M. Taiji, Y. Hirano, 2013 .

Femtosecond dynamics in rhodopsin

Takayoshi Kobayashi, M. Taiji, K. Bryl, 1993 .

Relaxation dynamics of photoexcitations in polydiacetylenes and polythiophene

Uwe Stamm, Makoto Taiji, Masayuki Yoshizawa, 1990 .

Relaxation dynamics of photoexcitations in polydiacetylene films

Makoto Taiji, Masayuki Yoshizawa, Takayoshi Kobayashi, 1989 .

Femtosecond to Microsecond Dynamics of Photoexcitations in a Polydiacetylene Film

M. Taiji, M. Yoshizawa, K. Ichimura, 1988 .

Novel Mechanism of Interaction of p85 Subunit of Phosphatidylinositol 3-Kinase and ErbB3 Receptor-derived Phosphotyrosyl Peptides*

Akihiko Konagaya, Makoto Taiji, Tetsu Narumi, 2005, Journal of Biological Chemistry.

A pre-metazoan origin of the CRK gene family and co-opted signaling network

T. Kigawa, M. Taiji, N. Okimoto, 2016, Scientific Reports.

Current performance gains from utilizing the GPU or the ASIC MDGRAPE‐3 within an enhanced Poisson Boltzmann approach

Makoto Taiji, Siegfried Höfinger, Tetsu Narumi, 2009, J. Comput. Chem..

Application of MDGRAPE‐3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems

Haruki Nakamura, Ryutaro Himeno, Makoto Taiji, 2009, J. Comput. Chem..

Femtosecond time-resolved interferometry for the determination of complex nonlinear susceptibility.

K. Minoshima, M. Taiji, T Kobayashi, 1991, Optics letters.

Molecular dynamics, free energy, and SPR analyses of the interactions between the SH2 domain of Grb2 and ErbB phosphotyrosyl peptides.

Akihiko Konagaya, Makoto Taiji, Tetsu Narumi, 2003, Biochemistry.

42 TFlops hierarchical N-body simulations on GPUs with applications in both astrophysics and turbulence

Makoto Taiji, Rio Yokota, Tsuyoshi Hamada, 2009, Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis.

Interfacial Layer Breaker: A Violation of Stokes’ Law in High-Speed Atomic Force Microscope Flows

S. Karabasov, M. Taiji, I. Korotkin, 2022, Langmuir : the ACS journal of surfaces and colloids.

A multi-scale and multi-physics Atomic Force Microscopy model for force 1 calculations at atomistic resolution and realistic flow conditions 2

S. Karabasov, M. Taiji, I. Korotkin, 2020 .

Aminoacyl-tRNA exclusively in the 3'-isomeric form is bound to polypeptide chain elongation factor Tu.

S. Yokoyama, M. Taiji, T. Miyazawa, 1985, Journal of biochemistry.

Femtosecond Spectroscopy of Polydiacetylene and Polythiophene

Takayoshi Kobayashi, K. Yoshino, M. Taiji, 1990 .

Evaluation of protein–ligand affinity prediction using steered molecular dynamics simulations

A. Suenaga, M. Taiji, N. Okimoto, 2017, Journal of biomolecular structure & dynamics.

Bead-like passage of chloride ions through ClC chloride channels.

A. Konagaya, K. Takayama, A. Suenaga, 2006, Biophysical chemistry.

High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations

Makoto Taiji, Tetsu Narumi, Yousuke Ohno, 2009, PLoS Comput. Biol..

Experimental identification and theoretical analysis of a thermally stabilized green fluorescent protein variant.

Takayuki Kobayashi, A. Suenaga, M. Taiji, 2012, Biochemistry.

A Highly Parallelized Special-Purpose Computer for Many-Body Simulations with an Arbitrary Central Force: MD-GRAPE

Toshikazu Ebisuzaki, Makoto Taiji, Toshiyuki Fukushige, 1996 .

FGF9 monomer/dimer equilibrium regulates extracellular matrix affinity and tissue diffusion

Makoto Taiji, Sachiko Iseki, Haruhiko Koseki, 2009, Nature Genetics.

Fast and accurate molecular dynamics simulation of a protein using a special‐purpose computer

Makoto Taiji, Yuto Komeiji, Masami Uebayasi, 1997 .

Petascale molecular dynamics simulation using the fast multipole method on K computer

Huda Ibeid, Makoto Taiji, Rio Yokota, 2014, Comput. Phys. Commun..

A Comparative Study on ASIC, FPGAs, GPUs and General Purpose Processors in the O(N^2) Gravitational N-body Simulation

Makoto Taiji, Tsuyoshi Hamada, Khaled Benkrid, 2009, 2009 NASA/ESA Conference on Adaptive Hardware and Systems.

GRAPE-4: a teraFLOPS massively parallel special-purpose computer system for astrophysical N-body simulations

Toshikazu Ebisuzaki, Makoto Taiji, Junichiro Makino, 1994, Proceedings of 8th International Parallel Processing Symposium.

Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations

T. Narumi, M. Taiji, Y. Ohno, 2003, ACM/IEEE SC 2003 Conference (SC'03).

A new set of atomic radii for accurate estimation of solvation free energy by Poisson–Boltzmann solvent model

Makoto Taiji, Gentaro Morimoto, Noriaki Okimoto, 2014, J. Comput. Chem..

Imitation and Cooperation in Coupled Dynamical Recognizers

Makoto Taiji, Takashi Ikegami, T. Ikegami, 1999, ECAL.

Tyr-317 Phosphorylation Increases Shc Structural Rigidity and Reduces Coupling of Domain Motions Remote from the Phosphorylation Site as Revealed by Molecular Dynamics Simulations*

B. Kholodenko, T. Ebisuzaki, A. Konagaya, 2004, Journal of Biological Chemistry.

Molecular Dynamics Study of Conformational Changes of Tankyrase 2 Binding Subsites upon Ligand Binding

M. Taiji, Y. Hirano, N. Okimoto, 2021, ACS omega.

A 281 Tflops calculation for X-ray protein structure analysis with special-purpose computers MDGRAPE-3

Toshikazu Ebisuzaki, Ryutaro Himeno, Makoto Taiji, 2007, Proceedings of the 2007 ACM/IEEE Conference on Supercomputing (SC '07).

All-Atom Molecular Dynamics Simulations of Entire Virus Capsid Reveal the Role of Ion Distribution in Capsid's Stability.

M. Taiji, N. Okimoto, R. Khayat, 2017, The journal of physical chemistry letters.

Structural relaxation and binding energy calculations of FK506 binding protein complexes using the large-scale DFT code CONQUEST

D. Bowler, T. Miyazaki, M. Taiji, 2013 .

Mutation of epidermal growth factor receptor is associated with MIG6 expression

Hiroshi Tanaka, Shih-Feng Tsai, Makoto Taiji, 2009, The FEBS journal.

Fluorogenic Enhancement of an in Vitro-Selected Peptide Ligand by Replacement of a Fluorescent Group.

Deqing Zhang, Guanxin Zhang, Yoshihiro Ito, 2016, Analytical chemistry.

A fluorogenic peptide probe developed by in vitro selection using tRNA carrying a fluorogenic amino acid.

N. Hayashi, T. Kigawa, Yoshihiro Ito, 2014, Chemical communications.

Scientific simulations with special purpose computers - the GRAPE systems

Makoto Taiji, Junichiro Makino, J. Makino, 1998 .

MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations

Makoto Taiji, Yousuke Ohno, Aki Hasegawa, 2014, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

Free-energy landscapes of protein domain movements upon ligand binding.

Makoto Taiji, Gentaro Morimoto, Hiroko X Kondo, 2011, The journal of physical chemistry. B.

A novel multiple-walk parallel algorithm for the Barnes–Hut treecode on GPUs – towards cost effective, high performance N-body simulation

Tomonari Masada, Yuichiro Shibata, Kiyoshi Oguri, 2009, Computer Science - Research and Development.

Details of charge distribution in stable viral capsid

M. Taiji, D. Nerukh, V. Farafonov, 2018, Journal of Molecular Liquids.

Computational astrophysics on a special-purpose machine

Makoto Taiji, Junichiro Makino, J. Makino, 1996 .

Ligand Diffusion on Protein Surface Observed in Molecular Dynamics Simulation.

Makoto Taiji, Dmitry Nerukh, Noriaki Okimoto, 2012, The journal of physical chemistry letters.

On the Power of Nonlinear Mappings in Switching Map Systems

Makoto Taiji, Takashi Ikegami, Yuzuru Sato, 2000, UMC.

Assessment and acceleration of binding energy calculations for protein–ligand complexes by the fragment molecular orbital method

Makoto Taiji, Takao Otsuka, Noriaki Okimoto, 2015, J. Comput. Chem..

A high performance system for molecular dynamics simulation of biomolecules using a special-purpose computer.

T Fukushige, D Sugimoto, M. Taiji, 1996, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

A 55 TFLOPS simulation of amyloid-forming peptides from yeast prion Sup35 with the special-purpose computer system MDGRAPE-3

Ryutaro Himeno, Makoto Taiji, Tetsu Narumi, 2006, SC.

Estimation of Ligand Binding Free Energies of F-ATPase by Using Molecular Dynamics/Free Energy Calculation

T. Ando, A. Suenaga, M. Taiji, 2008 .

Inaccessibility in online learning of recurrent neural networks.

Makoto Taiji, Takashi Ikegami, Asaki Saito, 2004, Physical review letters.

Folding dynamics of 10-residue beta-hairpin peptide chignolin.

Makoto Taiji, Tetsu Narumi, Yousuke Ohno, 2007, Chemistry, an Asian journal.

GRAPE-5: A Special-Purpose Computer for iV-Body Simulations

M. Taiji, T. Fukushige, A. Kawai, 2013 .

Reversible hydrogel formation driven by protein-peptide-specific interaction and chondrocyte entrapment.

Y. Hayashizaki, Harukazu Suzuki, M. Itoh, 2010, Biomaterials.

21-residue peptide's dynamics at and between elementary structural transitions

M. Taiji, D. Nerukh, 2009 .