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Shoji Takada

Shoji Takada

D-Index & Metrics

Biology and Biochemistry

D-Index
48
Citations
9033
World Ranking
18350
National Ranking
1319

Overview

Shoji Takada is affiliated with Kyoto University in Japan and has an extensive publication record in the field of Biochemistry, Genetics, and Molecular Biology. Their research primarily focuses on Molecular Biology and includes subfields such as Atomic and Molecular Physics and Optics, Cell Biology, Structural Biology, and Genetics.

Takada's work covers a range of scientific topics including:

  • Genomics and Chromatin Dynamics
  • RNA and protein synthesis mechanisms
  • RNA Research and Splicing
  • Force Microscopy Techniques and Applications
  • DNA and Nucleic Acid Chemistry
  • Protein Structure and Dynamics
  • Advanced Electron Microscopy Techniques and Applications

Their recent papers include:

  • "Nucleosome allostery in pioneer transcription factor binding," 2020, Proceedings of the National Academy of Sciences
  • "Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations," 2022, PLoS Computational Biology
  • "Flexible Fitting of Biomolecular Structures to Atomic Force Microscopy Images via Biased Molecular Simulations," 2020, Journal of Chemical Theory and Computation
  • "Molecular dynamics simulation of proton-transfer coupled rotations in ATP synthase FO motor," 2020, Scientific Reports
  • "Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov State Model," 2021, Proceedings of the National Academy of Sciences

Takada has collaborated frequently with several researchers including Giovanni B. Brandani, Toru Niina, Cheng Tan, Shintaroh Kubo, and Yuji Sugita. These coauthors have appeared collectively in numerous publications, reflecting ongoing research partnerships.

Their work has been published in a variety of scientific venues. The most frequent publication platforms include:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • Biophysical Journal
  • PLoS Computational Biology
  • Journal of Chemical Theory and Computation
  • Nucleic Acids Research

Best Publications

  • On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction

    Hiroaki Fukunishi;Osamu Watanabe;Shoji Takada

  • Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model.

    Nobuyasu Koga;Shoji Takada;Shoji Takada

  • Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms

    Kei-ichi Okazaki;Shoji Takada

  • Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations

    Kei-ichi Okazaki;Nobuyasu Koga;Shoji Takada;Jose N. Onuchic

  • Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins

    Tatsuya Niwa;Bei Wen Ying;Bei Wen Ying;Katsuyo Saito;Wenzhen Jin

  • How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: Molecular simulations

    Fumiko Takagi;Nobuyasu Koga;Shoji Takada

  • Coarse-grained molecular simulations of large biomolecules

    Shoji Takada

  • CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work

    Hiroo Kenzaki;Nobuyasu Koga;Naoto Hori;Ryo Kanada

  • Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and a random heteropolymer

    Shoji Takada;Shoji Takada;Zaida Luthey-Schulten;Peter G. Wolynes

  • Microscopic Theory of Protein Folding Rates.II: Local Reaction Coordinates and Chain Dynamics

    John J. Portman;Shoji Takada;Peter G. Wolynes

  • Go-ing for the prediction of protein folding mechanisms.

    Shoji Takada

  • Energy landscape views for interplays among folding, binding, and allostery of calmodulin domains

    Wenfei Li;Wei Wang;Shoji Takada

  • Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins

    Wenfei Li;Peter G. Wolynes;Shoji Takada

  • On easy implementation of a variant of the replica exchange with solute tempering in GROMACS.

    Tsuyoshi Terakawa;Tomoshi Kameda;Shoji Takada

  • Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knot

    Wenfei Li;Wenfei Li;Tsuyoshi Terakawa;Wei Wang;Shoji Takada

  • Variational Theory for Site Resolved Protein Folding Free Energy Surfaces

    J. J. Portman;S. Takada;P. G. Wolynes

  • Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations.

    Shoji Takada;Ryo Kanada;Cheng Tan;Tsuyoshi Terakawa

  • Folding-based molecular simulations reveal mechanisms of the rotary motor F1-ATPase.

    Nobuyasu Koga;Shoji Takada

  • Effects of vibrational excitation on multidimensional tunneling: General study and proton tunneling in tropolone

    Shoji Takada;Hiroki Nakamura

  • Optimizing physical energy functions for protein folding.

    Yoshimi Fujitsuka;Shoji Takada;Shoji Takada;Zaida A. Luthey-Schulten;Peter G. Wolynes

Frequent Co-Authors

Peter G. Wolynes
Peter G. Wolynes Rice University
Shun Hirota
Shun Hirota Nara Institute of Science and Technology
Masaru Tanokura
Masaru Tanokura University of Tokyo
Tsutomu Katayama
Tsutomu Katayama Kyushu University
Do Hyun Kim
Do Hyun Kim Korea Advanced Institute of Science and Technology
Reid C. Johnson
Reid C. Johnson University of California, Los Angeles
Hitoshi Kurumizaka
Hitoshi Kurumizaka University of Tokyo
Zaida Luthey-Schulten
Zaida Luthey-Schulten University of Illinois at Urbana-Champaign
Soichi Wakatsuki
Soichi Wakatsuki Stanford University
Shaul Mukamel
Shaul Mukamel University of California, Irvine

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