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Informational thermodynamics of biomolecular crowding systems in water

Planned Research

Project AreaChemical Approaches for Miscellaneous / Crowding Live Systems
Project/Area Number 17H06353
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Science and Engineering
Research InstitutionKobe University

Principal Investigator

Tanaka Shigenori  神戸大学, システム情報学研究科, 教授 (10379480)

Project Period (FY) 2017-06-30 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥62,790,000 (Direct Cost: ¥48,300,000、Indirect Cost: ¥14,490,000)
Fiscal Year 2021: ¥11,700,000 (Direct Cost: ¥9,000,000、Indirect Cost: ¥2,700,000)
Fiscal Year 2020: ¥11,700,000 (Direct Cost: ¥9,000,000、Indirect Cost: ¥2,700,000)
Fiscal Year 2019: ¥11,700,000 (Direct Cost: ¥9,000,000、Indirect Cost: ¥2,700,000)
Fiscal Year 2018: ¥11,700,000 (Direct Cost: ¥9,000,000、Indirect Cost: ¥2,700,000)
Fiscal Year 2017: ¥15,990,000 (Direct Cost: ¥12,300,000、Indirect Cost: ¥3,690,000)
Keywords分子夾雑 / 分子動力学法 / 生体高分子 / 会合解離 / 自由エネルギー / アミロイド / 熱伝導 / 量子生命科学 / 細胞内分子夾雑 / タンパク質多量体 / 非平衡解離過程 / 加水分解反応 / 発熱反応 / 温度緩和 / エネルギー移動 / 細胞内夾雑環境 / 情報熱力学 / 量子性 / 水 / 解離会合過程 / モンテカルロ法 / 第一原理計算 / 生体分子 / 非平衡熱力学 / 生命の起源 / ハイパフォーマンス・コンピューティング / 蛋白質 / 核酸 / 分子認識 / システム生物学
Outline of Final Research Achievements

In response to the question of "how the intracellular molecular crowding environment affects the functional expression of biomolecules", we have developed computational methods to efficiently describe the processes of association and dissociation of protein multimers mainly based on the molecular dynamics (MD) simulation. We thus performed actual application calculations, and quantitatively elucidated their molecular mechanisms. Specifically, we targeted amyloid aggregates involved in neurological diseases and Ras protein complexes related to cancer. In addition to describing their association / dissociation dynamics thermodynamically from the viewpoint of free energy and thermal energy, the roles played by substrates such as ATP and GTP were also microscopically elucidated. Furthermore, we also tried to theoretically describe heat conduction, temperature relaxation, and quantum characteristics in biomolecular systems.

Academic Significance and Societal Importance of the Research Achievements

従来の分子生物学・細胞生物学は分子レベルから生命機能を解き明かす上で重要な多くの知見を蓄積してきたが、細胞内の分子夾雑環境が果たす役割については未解明の部分が多かった。本研究では特に、タンパク質や核酸などの生体高分子が形成する複合体に注目し、その形成や崩壊などの過程が微視的にどのように起きるのかを可視化・定量化する計算機シミュレーション技術を開発した。また、それに基づき、アルツハイマー病やガンなどに関わる分子系の応用計算を行い、細胞内のATPやGTPなどの共存分子が演じる役割についても新たな知見を得た。加えて、温度生物学や情報熱力学、量子生命科学などの新たな学術領域への展開も試みた。

Report

(6 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • Research Products

    (66 results)

All 2022 2021 2020 2019 2018 2017 Other

All Int'l Joint Research (2 results) Journal Article (44 results) (of which Int'l Joint Research: 14 results,  Peer Reviewed: 44 results,  Open Access: 23 results,  Acknowledgement Compliant: 4 results) Presentation (15 results) (of which Int'l Joint Research: 5 results,  Invited: 15 results) Book (3 results) Remarks (2 results)

  • [Int'l Joint Research] カールスルーエ工科大学(ドイツ)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] カールスルーエ工科大学(ドイツ)

    • Related Report
      2018 Annual Research Report
  • [Journal Article] Remarked suppression of Aβ42 protomer-protomer dissociation reaction elucidated by molecular dynamics simulation2022

    • Author(s)
      Kurisaki Ikuo、Tanaka Shigenori
    • Journal Title

      Proteins: Structure, Function, and Bioinformatics

      Volume: 2022 Issue: 7 Pages: 1-9

    • DOI

      10.1002/prot.26319

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Computational prediction of heteromeric protein complex disassembly order using hybrid Monte Carlo/molecular dynamics simulation2022

    • Author(s)
      Kurisaki Ikuo、Tanaka Shigenori
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 24 Issue: 17 Pages: 10575-10587

    • DOI

      10.1039/d2cp00267a

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Reaction Pathway Sampling and Free-Energy Analyses for Multimeric Protein Complex Disassembly by Employing Hybrid Configuration Bias Monte Carlo/Molecular Dynamics Simulation2021

    • Author(s)
      Kurisaki Ikuo、Tanaka Shigenori
    • Journal Title

      ACS Omega

      Volume: 6 Issue: 7 Pages: 4749-4758

    • DOI

      10.1021/acsomega.0c05579

    • NAID

      120007026370

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses2021

    • Author(s)
      Watanabe Chiduru、Okiyama Yoshio、Tanaka Shigenori、Fukuzawa Kaori、Honma Teruki
    • Journal Title

      Chemical Science

      Volume: 12 Issue: 13 Pages: 4722-4739

    • DOI

      10.1039/d0sc06528e

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Statistical interaction analyses between SARS-CoV-2 main protease and inhibitor N3 by combining molecular dynamics simulation and fragment molecular orbital calculation2021

    • Author(s)
      Hatada Ryo、Okuwaki Koji、Akisawa Kazuki、Mochizuki Yuji、Handa Yuma、Fukuzawa Kaori、Komeiji Yuto、Okiyama Yoshio、Tanaka Shigenori
    • Journal Title

      Applied Physics Express

      Volume: 14 Issue: 2 Pages: 027003-027003

    • DOI

      10.35848/1882-0786/abdac6

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] In silico modeling of PAX8-PPARγ fusion protein in thyroid carcinoma: influence of structural perturbation by fusion on ligand-binding affinity2021

    • Author(s)
      Sakaguchi Kaori、Okiyama Yoshio、Tanaka Shigenori
    • Journal Title

      Journal of Computer-Aided Molecular Design

      Volume: 35 Issue: 5 Pages: 629-642

    • DOI

      10.1007/s10822-021-00381-x

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Density-Matrix Based Scheme of Basis Selection for Linear Combination of Fragment Molecular Orbitals2021

    • Author(s)
      Okiyama Yoshio、Mochizuki Yuji、Yamanaka Masanori、Tanaka Shigenori
    • Journal Title

      Journal of the Physical Society of Japan

      Volume: 90 Issue: 6 Pages: 064301-064301

    • DOI

      10.7566/jpsj.90.064301

    • NAID

      40022591155

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Dynamic Cooperativity of Ligand?Residue Interactions Evaluated with the Fragment Molecular Orbital Method2021

    • Author(s)
      Tanaka Shigenori、Tokutomi Shusuke、Hatada Ryo、Okuwaki Koji、Akisawa Kazuki、Fukuzawa Kaori、Komeiji Yuto、Okiyama Yoshio、Mochizuki Yuji
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 125 Issue: 24 Pages: 6501-6512

    • DOI

      10.1021/acs.jpcb.1c03043

    • NAID

      120007170803

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Fragment molecular orbital based interaction analyses on complexes between SARS-CoV-2 RBD variants and ACE22021

    • Author(s)
      Akisawa Kazuki、Hatada Ryo、Okuwaki Koji、Kitahara Shun、Tachino Yusuke、Mochizuki Yuji、Komeiji Yuto、Tanaka Shigenori
    • Journal Title

      Japanese Journal of Applied Physics

      Volume: 60 Issue: 9 Pages: 090901-090901

    • DOI

      10.35848/1347-4065/ac1857

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Appearance of Thermal Time2021

    • Author(s)
      Tanaka Shigenori
    • Journal Title

      Foundations of Physics

      Volume: 51 Issue: 2 Pages: 34-34

    • DOI

      10.1007/s10701-021-00445-w

    • NAID

      120007026363

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Non-equilibrium Quantum Brain Dynamics II: Formulation in 3+1 dimensions2021

    • Author(s)
      Nishiyama Akihiro、Tanaka Shigenori、Tuszynski Jack A.
    • Journal Title

      Physica A: Statistical Mechanics and its Applications

      Volume: 567 Pages: 125706-125706

    • DOI

      10.1016/j.physa.2020.125706

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Improvement of the Force Field for β-d-Glucose with Machine Learning2021

    • Author(s)
      Ikejo Makoto、Watanabe Hirofumi、Shimamura Kohei、Tanaka Shigenori
    • Journal Title

      Molecules

      Volume: 26 Issue: 21 Pages: 6691-6691

    • DOI

      10.3390/molecules26216691

    • NAID

      120007170798

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Elucidating microscopic events driven by GTP hydrolysis reaction in the Ras-GAP system with semi-reactive molecular dynamics simulations: the alternative role of a phosphate binding loop for mechanical energy storage2021

    • Author(s)
      Kurisaki Ikuo、Tanaka Shigenori
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 23 Issue: 46 Pages: 26151-26164

    • DOI

      10.1039/d1cp04061h

    • NAID

      120007179185

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Collective residue interactions in trimer complexes of SARS-CoV-2 spike proteins analyzed by fragment molecular orbital method2021

    • Author(s)
      Okuwaki Koji、Akisawa Kazuki、Hatada Ryo、Mochizuki Yuji、Fukuzawa Kaori、Komeiji Yuto、Tanaka Shigenori
    • Journal Title

      Applied Physics Express

      Volume: 15 Issue: 1 Pages: 017001-017001

    • DOI

      10.35848/1882-0786/ac4300

    • NAID

      120007181729

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] FMODB: The World’s First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method2021

    • Author(s)
      Daisuke Takaya, Chiduru Watanabe, Shunpei Nagase, Kikuko Kamisaka, Yoshio Okiyama, Hirotomo Moriwaki, Hitomi Yuki, Tomohiro Sato, Noriyuki Kurita, Yoichiro Yagi, Tatsuya Takagi, Norihito Kawashita, Kenichiro Takaba, Tomonaga Ozawa, Midori Takimoto-Kamimura, Shigenori Tanaka, Kaori Fukuzawa, and Teruki Honma
    • Journal Title

      J. Chem. Inf. Model.

      Volume: 61 Issue: 2 Pages: 777-794

    • DOI

      10.1021/acs.jcim.0c01062

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Interaction analyses of SARS-CoV-2 spike protein based on fragment molecular orbital calculations2021

    • Author(s)
      Akisawa Kazuki、Hatada Ryo、Okuwaki Koji、Mochizuki Yuji、Fukuzawa Kaori、Komeiji Yuto、Tanaka Shigenori
    • Journal Title

      RSC Advances

      Volume: 11 Issue: 6 Pages: 3272-3279

    • DOI

      10.1039/d0ra09555a

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Comparative study on model parameter evaluations for the energy transfer dynamics in Fenna?Matthews?Olson complex2020

    • Author(s)
      Suzuki Yosuke、Watanabe Hirofumi、Okiyama Yoshio、Ebina Kuniyoshi、Tanaka Shigenori
    • Journal Title

      Chemical Physics

      Volume: 539 Pages: 110903-110903

    • DOI

      10.1016/j.chemphys.2020.110903

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Machine learning prediction of inter-fragment interaction energies between ligand and amino-acid residues on the fragment molecular orbital calculations for Janus kinase ? inhibitor complex2020

    • Author(s)
      Tokutomi Shusuke、Shimamura Kohei、Fukuzawa Kaori、Tanaka Shigenori
    • Journal Title

      Chemical Physics Letters

      Volume: 757 Pages: 137883-137883

    • DOI

      10.1016/j.cplett.2020.137883

    • NAID

      120006890795

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Identification of correlated inter-residue interactions in protein complex based on the fragment molecular orbital method2020

    • Author(s)
      Tanaka Shigenori、Watanabe Chiduru、Honma Teruki、Fukuzawa Kaori、Ohishi Kazue、Maruyama Tadashi
    • Journal Title

      Journal of Molecular Graphics and Modelling

      Volume: 100 Pages: 107650-107650

    • DOI

      10.1016/j.jmgm.2020.107650

    • NAID

      120006890786

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Temperature relaxation in binary hard-sphere mixture system: Molecular dynamics and kinetic theory study2020

    • Author(s)
      Tanaka Shigenori、Shimamura Kohei
    • Journal Title

      The Journal of Chemical Physics

      Volume: 153 Issue: 3 Pages: 034114-034114

    • DOI

      10.1063/5.0011181

    • NAID

      120006879543

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease ? Inhibitor N3 Complex (PDB ID: 6LU7)2020

    • Author(s)
      Hatada Ryo、Okuwaki Koji、Mochizuki Yuji、Handa Yuma、Fukuzawa Kaori、Komeiji Yuto、Okiyama Yoshio、Tanaka Shigenori
    • Journal Title

      Journal of Chemical Information and Modeling

      Volume: 60 Issue: 7 Pages: 3593-3602

    • DOI

      10.1021/acs.jcim.0c00283

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Effective Static Approximation: A Fast and Reliable Tool for Warm-Dense Matter Theory2020

    • Author(s)
      Dornheim Tobias、Cangi Attila、Ramakrishna Kushal、B?hme Maximilian、Tanaka Shigenori、Vorberger Jan
    • Journal Title

      Physical Review Letters

      Volume: 125 Issue: 23 Pages: 235001-235001

    • DOI

      10.1103/physrevlett.125.235001

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] New Modified Deoxythymine with Dibranched Tetraethylene Glycol Stabilizes G-quadruplex Structures2020

    • Author(s)
      H. Tateishi-Karimata, T. Ohyama, T. Muraoka, S. Tanaka, K. Kinbara, and N. Sugimoto
    • Journal Title

      Molecules

      Volume: 25 Issue: 3 Pages: 705-705

    • DOI

      10.3390/molecules25030705

    • NAID

      120006811187

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Strongly Coupled Electron Liquid: Ab Initio Path Integral Monte Carlo Simulations and Dielectric Theories2020

    • Author(s)
      T. Dornheim, T. Sjostrom, S. Tanaka, and J. Vorberger
    • Journal Title

      Phys. Rev. B

      Volume: 101 Issue: 4 Pages: 045129-045129

    • DOI

      10.1103/physrevb.101.045129

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Non-Equilibrium Quantum Electrodynamics in Open Systems as a Realizable Representation of Quantum Field Theory of the Brain2020

    • Author(s)
      A. Nishiyama, S. Tanaka, and J.A. Tuszynski
    • Journal Title

      Entropy

      Volume: 22 Issue: 1 Pages: 43-43

    • DOI

      10.3390/e22010043

    • NAID

      120006823996

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] <b>Development of an automated fragment molecular orbital (FMO) calculation protocol toward construction of quantum mechanical </b><b>calculation database for large biomolecules </b>2019

    • Author(s)
      Watanabe Chiduru、Watanabe Hirofumi、Okiyama Yoshio、Takaya Daisuke、Fukuzawa Kaori、Tanaka Shigenori、Honma Teruki
    • Journal Title

      Chem-Bio Informatics Journal

      Volume: 19 Issue: 0 Pages: 5-18

    • DOI

      10.1273/cbij.19.5

    • NAID

      130007618360

    • ISSN
      1347-0442, 1347-6297
    • Year and Date
      2019-03-22
    • Related Report
      2019 Annual Research Report 2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Ab Initio Molecular Dynamics Study of Prebiotic Production Processes of Organic Compounds at Meteorite Impacts on Ocean2019

    • Author(s)
      K. Shimamura, F. Shimojo, A. Nakano, and S. Tanaka
    • Journal Title

      Journal of Computational Chemistry

      Volume: 40 Issue: 2 Pages: 349-359

    • DOI

      10.1002/jcc.25606

    • NAID

      120006734928

    • Related Report
      2019 Annual Research Report 2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson-Boltzmann Equation: II. Protein and Its Ligand-Binding System Studies2019

    • Author(s)
      Y. Okiyama, C. Watanabe, K. Fukuzawa, Y. Mochizuki, T. Nakano, S. Tanaka
    • Journal Title

      J. Phys. Chem. B

      Volume: 123 Issue: 5 Pages: 957-973

    • DOI

      10.1021/acs.jpcb.8b09326

    • Related Report
      2019 Annual Research Report 2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Non-Equilibrium Quantum Brain Dynamics: Super-Radiance and Equilibration in 2+1 Dimensions2019

    • Author(s)
      A. Nishiyama, S. Tanaka, and J.A. Tuszynski
    • Journal Title

      Entropy

      Volume: 21 Issue: 11 Pages: 1066-1066

    • DOI

      10.3390/e21111066

    • NAID

      120006777079

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] ATP Converts Aβ42 Oligomer into Off-Pathway Species by Making Contact with Its Backbone Atoms Using Hydrophobic Adenosine2019

    • Author(s)
      I. Kurisaki and S. Tanaka
    • Journal Title

      J. Phys. Chem. B

      Volume: 123 Issue: 46 Pages: 9922-9933

    • DOI

      10.1021/acs.jpcb.9b07984

    • NAID

      120006775976

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Guidelines for Creating Artificial Neural Network Empirical Interatomic Potential from First-Principles Molecular Dynamics Data under Specific Conditions and Its Application to α-Ag2Se2019

    • Author(s)
      K. Shimamura, S. Fukushima, A. Koura, F. Shimojo, M. Misawa, R.K. Kalia, A. Nakano, P. Vashishta, T. Matsubara, and S. Tanaka
    • Journal Title

      J. Chem. Phys.

      Volume: 151 Issue: 12 Pages: 124303-124303

    • DOI

      10.1063/1.5116420

    • NAID

      120006734929

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Application of singular value decomposition to the inter-fragment interaction energy analysis for ligand screening2018

    • Author(s)
      Maruyama Keiya、Sheng Yinglei、Watanabe Hirofumi、Fukuzawa Kaori、Tanaka Shigenori
    • Journal Title

      Computational and Theoretical Chemistry

      Volume: 1132 Pages: 23-34

    • DOI

      10.1016/j.comptc.2018.04.001

    • NAID

      120006482609

    • Related Report
      2019 Annual Research Report 2018 Annual Research Report 2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Towards Good Correlation between Fragment Molecular Orbital Interaction Energies and Experimental IC50 for Ligand Binding: A Case Study of p38 MAP Kinase2018

    • Author(s)
      Y. Sheng, H. Watanabe, K. Maruyama, C. Watanabe, Y. Okiyama, T. Honma, K. Fukuzawa, S. Tanaka
    • Journal Title

      Comput. Struct. Biotech. J.

      Volume: 16 Pages: 421-434

    • DOI

      10.1016/j.csbj.2018.10.003

    • NAID

      120006549198

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Computational Analysis of the Interaction Energies between Amino Acid Residues of the Measles Virus Hemagglutinin and Its Receptors2018

    • Author(s)
      F. Xu, S. Tanaka, H. Watanabe, Y. Shimane, M. Iwasawa, K. Ohishi, T. Maruyama
    • Journal Title

      Viruses

      Volume: 10 Issue: 5 Pages: 236-236

    • DOI

      10.3390/v10050236

    • NAID

      120006488447

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson?Boltzmann Equation: Implementation and DNA Study2018

    • Author(s)
      Okiyama Yoshio、Nakano Tatsuya、Watanabe Chiduru、Fukuzawa Kaori、Mochizuki Yuji、Tanaka Shigenori
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 122 Issue: 16 Pages: 4457-4471

    • DOI

      10.1021/acs.jpcb.8b01172

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Pursuing origins of (poly)ethylene glycol-induced G-quadruplex structural modulations2018

    • Author(s)
      M. Trajkovski, T. Endoh, H. Tateishi-Karimata, T. Ohyama, S. Tanaka, J. Plavec, N. Sugimoto
    • Journal Title

      Nucleic Acids Research

      Volume: 46 Issue: 8 Pages: 4301-4315

    • DOI

      10.1093/nar/gky250

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Newly characterized interaction stabilizes DNA structure: oligoethylene glycols stabilize G-quadruplexes CH?π interactions2017

    • Author(s)
      Tateishi-Karimata Hisae、Ohyama Tatsuya、Muraoka Takahiro、Podbevsek Peter、Wawro Adam M.、Tanaka Shigenori、Nakano Shu-ichi、Kinbara Kazushi、Plavec Janez、Sugimoto Naoki
    • Journal Title

      Nucleic Acids Research

      Volume: 45 Issue: 12 Pages: 7021-7030

    • DOI

      10.1093/nar/gkx299

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] An Effective Microscopic Index Associated with Cell Survival and DNA Lesions for Estimating Radiation Risk2017

    • Author(s)
      K. Yoshinari, S. Tanaka, K. Ebina
    • Journal Title

      J. Environ. Health Sci.

      Volume: 3 Issue: 1 Pages: 1-5

    • DOI

      10.15436/2378-6841.17.1187

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Improved Equation of State for Finite-Temperature Spin-Polarized Electron Liquids on the Basis of Singwi-Tosi-Land-Sjolander Approximation2017

    • Author(s)
      S. Tanaka
    • Journal Title

      Contrib. Plasma Phys.

      Volume: 57 Issue: 3 Pages: 126-136

    • DOI

      10.1002/ctpp.201600096

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Cosolvent-Based Molecular Dynamics for Ensemble Docking: Practical Method for Generating Druggable Protein Conformations2017

    • Author(s)
      S. Uehara, S. Tanaka
    • Journal Title

      J. Chem. Inf. Model.

      Volume: 57 Issue: 4 Pages: 742-756

    • DOI

      10.1021/acs.jcim.6b00791

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Meteorite impacts on ancient oceans opened up multiple NH3 production pathways2017

    • Author(s)
      Kohei Shimamura, Fuyuki Shimojo, Aiichiro Nakano, and Shigenori Tanaka
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 印刷中 Issue: 18 Pages: 11655-11667

    • DOI

      10.1039/c7cp00870h

    • NAID

      120006318803

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Structural transition of solvated H-Ras/GTP revealed by molecular dynamics simulation and local network entropy2017

    • Author(s)
      Matsunaga Shota、Hano Yuta、Saito Yuta、Fujimoto Kazuhiro J.、Kumasaka Takashi、Matsumoto Shigeyuki、Kataoka Tohru、Shima Fumi、Tanaka Shigenori
    • Journal Title

      Journal of Molecular Graphics and Modelling

      Volume: 77 Pages: 51-63

    • DOI

      10.1016/j.jmgm.2017.07.028

    • NAID

      120006406708

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Information Geometrical Characterization of the Onsager-Machlup Process2017

    • Author(s)
      S. Tanaka
    • Journal Title

      Chem. Phys. Lett.

      Volume: 689 Pages: 152-155

    • DOI

      10.1016/j.cplett.2017.10.005

    • NAID

      120006375911

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Theoretical Analysis of Activity Cliffs among Benzofuranone Class Pim1 Inhibitors Using the Fragment Molecular Orbital Method with Molecular Mechanics Poisson-Boltzmann Surface Area (FMO+MM-PBSA) Approach2017

    • Author(s)
      C. Watanabe, H. Watanabe, K. Fukuzawa, L. Parker, Y. Okiyama, H. Yuki, S. Yokoyama, H. Nakano, S. Tanaka, T. Honma
    • Journal Title

      J. Chem. Inf. Model.

      Volume: 57 Issue: 12 Pages: 2996-3010

    • DOI

      10.1021/acs.jcim.7b00110

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Presentation] Dynamical Association/Dissociation Processes of Biomolecules in Crowding Conditions2022

    • Author(s)
      Shigenori Tanaka
    • Organizer
      2nd International Symposium on Chemistry for Multimolecular Crowding Biosystems (CMCB2022)
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Fragment Molecular Orbital Calculations for SARS-CoV-2 Proteins2021

    • Author(s)
      Shigenori Tanaka
    • Organizer
      The 3rd R-CCS International Symposium
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] ナノ空間での熱伝導・温度緩和:温度生物学の基礎として2020

    • Author(s)
      田中成典
    • Organizer
      Biothermology Workshop 2020
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] 生命と量子2019

    • Author(s)
      田中成典
    • Organizer
      JST-CREST「生命動態の理解と制御のための基盤技術の創出」研究領域・第12回数理デザイン道場
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 多体問題と生命2019

    • Author(s)
      田中成典
    • Organizer
      研究会「計算生命科学:多体問題から生命システムへ」
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Perspectives of Computational Drug Discovery: AMED-BINDS Activities in Japan2019

    • Author(s)
      S. Tanaka
    • Organizer
      AHeDD2019/IPAB2019 Joint Symposium
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Quantum Brain Dynamics from a Viewpoint of Field Theory2019

    • Author(s)
      S. Tanaka and A. Nishiyama
    • Organizer
      The 2nd Workshop on Quantum Cognition
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] FMOデータベースの情報科学的な活用2019

    • Author(s)
      田中成典
    • Organizer
      日本薬学会第139年会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] ライフサイエンスと量子コンピューティング2018

    • Author(s)
      田中成典
    • Organizer
      第25回バイオメディカル研究会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] BINDSインシリコユニットの紹介2018

    • Author(s)
      田中成典
    • Organizer
      CBI学会2018年大会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] インシリコ創薬の展望2018

    • Author(s)
      田中成典
    • Organizer
      第56回日本生物物理学会年会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] バイオシミュレーションにおける分子夾雑効果2017

    • Author(s)
      田中成典
    • Organizer
      日本化学会第97春季年会・特別企画「分子夾雑の生命化学」
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 量子生命科学の展望2017

    • Author(s)
      田中成典
    • Organizer
      第1回量子生命科学研究会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Charge and Energy Transfer Dynamics in Biological Systems2017

    • Author(s)
      S. Tanaka
    • Organizer
      1st QST International Symposium “Quantum Life Science”
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 量子生命科学の展望2017

    • Author(s)
      田中成典
    • Organizer
      科学基礎論学会2017年度秋の研究例会シンポジウム「生命科学および認知科学における量子論的アプローチ」
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Book] Recent Advances of the Fragment Molecular Orbital Method: Enhanced Performance and Applicability2021

    • Author(s)
      Y. Mochizuki, S. Tanaka, K. Fukuzawa
    • Total Pages
      616
    • Publisher
      Springer
    • ISBN
      9789811592348
    • Related Report
      2021 Annual Research Report
  • [Book] Entropy-Enthalpy Compensation: Finding a Methodological Common Denominator through Probability, Statistics, and Physics2021

    • Author(s)
      E.B. Starikov, B. Norden, S. Tanaka
    • Total Pages
      398
    • Publisher
      Jenny Stanford Publishing
    • ISBN
      9789814877305
    • Related Report
      2021 Annual Research Report
  • [Book] 計算分子生物学:物質科学からのアプローチ2018

    • Author(s)
      田中成典
    • Total Pages
      184
    • Publisher
      内田老鶴圃
    • ISBN
      9784753623136
    • Related Report
      2018 Annual Research Report
  • [Remarks] 神戸大学大学院システム情報学研究科計算科学専攻田中研究室ホームページ

    • URL

      http://eniac.scitec.kobe-u.ac.jp/tanaka/

    • Related Report
      2021 Annual Research Report 2020 Annual Research Report
  • [Remarks] 神戸大学田中研究室ホームページ

    • URL

      http://eniac.scitec.kobe-u.ac.jp/tanaka/

    • Related Report
      2019 Annual Research Report 2018 Annual Research Report

URL: 

Published: 2017-07-04   Modified: 2023-01-30  

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