World's Best Scientists 2026 revealed!
Haruki Nakamura

Haruki Nakamura

D-Index & Metrics

Chemistry

D-Index
84
Citations
28726
World Ranking
2787
National Ranking
156

Biology and Biochemistry

D-Index
87
Citations
30398
World Ranking
2808
National Ranking
176

Overview

Haruki Nakamura is affiliated with Osaka University in Japan and has contributed to various areas within molecular biology, spectroscopy, atomic and molecular physics, optics, biomedical engineering, and materials chemistry. Their work encompasses multiple subfields and intersects with both experimental and computational techniques.

Their recent publications highlight research across diverse scientific domains. Notable papers include:

  • The dominance model for heterosis explains culm length genetics in a hybrid sorghum variety (2021, Scientific Reports)
  • Relationship between Autistic Traits and Nutrient Intake among Japanese Children and Adolescents (2020, Nutrients)
  • Quantum chemical studies on hydrogen bonds in helical secondary structures (2022, Biophysical Reviews)
  • Real-time personal healthcare data analysis using edge computing for multimodal wearable sensors (2024, Device)
  • Molecular Interaction Mechanism of a 14-3-3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational Sampling (2020, Journal of Chemical Information and Modeling)

Nakamura frequently collaborates with several coauthors, underscoring interdisciplinary teamwork. Frequent collaborators include:

  • Hiromasa Tsujiguchi
  • Thao Thi Thu Nguyen
  • Akinori Hara
  • Sakae Miyagi
  • Yukari Shimizu

Their publication venues concentrate in journals that focus on biophysics, chemical information, and nutritional science. Key venues are:

  • Biophysics and Physicobiology (11 publications)
  • Biophysical Reviews (10 publications)
  • Scientific Reports (3 publications)
  • Nutrients (3 publications)
  • Research Square (3 publications)

Nakamura's research topics address complex biochemical and biophysical phenomena as well as technological applications. The main focus areas include:

  • Protein Structure and Dynamics
  • Environmental Monitoring and Data Management
  • Mass Spectrometry Techniques and Applications
  • Advanced Chemical Physics Studies
  • Advanced Sensor and Energy Harvesting Materials
  • Computational Drug Discovery Methods
  • Chemical Synthesis and Analysis

This body of work reflects a multidisciplinary approach integrating molecular biology concepts with advanced sensor technologies and computational methods suitable for both fundamental understanding and practical healthcare applications.

Best Publications

  • Announcing the worldwide Protein Data Bank.

    Helen Berman;Kim Henrick;Haruki Nakamura

  • The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

    Helen M. Berman;Kim Henrick;Haruki Nakamura;John L. Markley

  • Protein Data Bank: the single global archive for 3D macromolecular structure data

    Stephen K Burley;Helen M Berman;Charmi Bhikadiya

  • Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.

    Stephen K. Burley;Stephen K. Burley;Helen M. Berman;Gerard J. Kleywegt;John L. Markley

  • Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay.

    Kazufumi Matsushita;Osamu Takeuchi;Daron M. Standley;Yutaro Kumagai

  • Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices.

    Kazuhiro Ogata;Souichi Morikawa;Haruki Nakamura;Ai Sekikawa

  • Roles of electrostatic interaction in proteins.

    Haruki Nakamura

  • The cavity in the hydrophobic core of Myb DNA-binding domain is reserved for DNA recognition and trans-activation.

    Kazuhiro Ogata;Chie Kanei-Ishii;Motoko Sasaki;Hideki Hatanaka

  • Atomic structure of the RuvC resolvase: A holliday junction-specific endonuclease from E. coli

    Mariko Ariyoshi;Dmitry G. Vassylyev;Hiroshi Iwasaki;Haruki Nakamura

  • Solution structure of a DNA-binding unit of Myb: a helix-turn-helix-related motif with conserved tryptophans forming a hydrophobic core.

    Kazuhiro Ogata;Hironobu Hojo;Saburo Aimoto;Takahisa Nakai

  • An effective solvation term based on atomic occupancies for use in protein simulations

    Pieter F. W. Stouten;Cornelius Frömmel;Haruki Nakamura;Chris Sander

  • Disordered domains and high surface charge confer hubs with the ability to interact with multiple proteins in interaction networks.

    Ashwini Patil;Haruki Nakamura

  • Computer-aided antibody design.

    Daisuke Kuroda;Hiroki Shirai;Matthew P. Jacobson;Haruki Nakamura

  • Segmental isotope labeling for protein NMR using peptide splicing

    Toshio Yamazaki;Takanori Otomo;Natsuko Oda;Yoshimasa Kyogoku

  • How does RNase H recognize a DNA.RNA hybrid

    H Nakamura;Y Oda;S Iwai;H Inoue

  • Structural details of ribonuclease H from Escherichia coli as refined to an atomic resolution.

    K. Katayanagi;M. Miyagawa;M. Matsushima;M. Ishikawa

  • Structural classification of CDR-H3 in antibodies

    Hiroki Shirai;Akinori Kidera;Haruki Nakamura

  • Validation of Structures in the Protein Data Bank

    Swanand Gore;Eduardo Sanz García;Pieter M.S. Hendrickx;Aleksandras Gutmanas

  • Comparison of the free and DNA-complexed forms of the DNA-binding domain from c-Myb.

    Kazuhiro Ogata;Souichi Morikawa;Haruki Nakamura;Hironobu Hojo

  • H3-rules: identification of CDR-H3 structures in antibodies.

    Hiroki Shirai;Akinori Kidera;Haruki Nakamura

Frequent Co-Authors

Kengo Kinoshita
Kengo Kinoshita Tohoku University
Helen M. Berman
Helen M. Berman Rutgers, The State University of New Jersey
John L. Markley
John L. Markley University of Wisconsin–Madison
Kizashi Yamaguchi
Kizashi Yamaguchi Osaka University
Gerard J. Kleywegt
Gerard J. Kleywegt European Bioinformatics Institute
Stephen K. Burley
Stephen K. Burley Rutgers, The State University of New Jersey
Yoshifumi Nishimura
Yoshifumi Nishimura Hiroshima University
Mitsutaka Okumura
Mitsutaka Okumura Osaka University
Shigenori Kanaya
Shigenori Kanaya Osaka University
Sameer Velankar
Sameer Velankar European Bioinformatics Institute

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