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Development of theoretical methods for interaction analysis of protein-ligand systems in computational drug design

Research Project

Project/Area Number 26460035
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Physical pharmacy
Research InstitutionKobe University

Principal Investigator

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

Co-Investigator(Renkei-kenkyūsha) TSURUTA Hiroki  神戸大学, 学術・産業イノベーション創造本部, 准教授 (20346282)
Project Period (FY) 2014-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2016: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2015: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2014: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
Keywordsインシリコ創薬 / リガンドドッキング / 電子状態計算 / 相互作用解析 / クラスター分析 / ハイパフォーマンスコンピューティング / フラグメント分子軌道法 / 産官学連携
Outline of Final Research Achievements

In order to construct a platform of the structure-based insilico drug design, ab initio large-scale quamtum-chemical calculations for protein-ligand systems were carried out on the basis of the fragment molecular orbital (FMO) method. As one of our activities in the "FMO Drug Design Consortium" for the collaborations of industry, academia and government, the interaction analyses for cancer-related kinase p38 in complex with about one-hundred species of ligand molecules were performed, and the data base of the calculated results was constructed. In addition, the molecular dynamics simulations for the state transitions of cancer-related Ras protein were also carried out to investigate the open-close mechanism of molecular switches, which has provided useful information for the design of effective inhibitors for Ras.

Report

(4 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • 2014 Research-status Report
  • Research Products

    (50 results)

All 2017 2016 2015 2014 Other

All Int'l Joint Research (1 results) Journal Article (27 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 27 results,  Acknowledgement Compliant: 17 results,  Open Access: 3 results) Presentation (15 results) (of which Int'l Joint Research: 2 results,  Invited: 15 results) Book (1 results) Remarks (6 results)

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

    • Related Report
      2016 Annual Research Report
  • [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
      2016 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
      2016 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
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Diffusion Monte Carlo Study on Temporal Evolution of Entropy and Free Energy in Nonequilibrium Processes2016

    • Author(s)
      S. Tanaka
    • Journal Title

      J. Chem. Phys.

      Volume: 144 Issue: 9 Pages: 094103-094103

    • DOI

      10.1063/1.4942861

    • NAID

      120005842522

    • Related Report
      2016 Annual Research Report 2015 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Reduced Minimum Model for the Photosynthetic Induction Processes in Photosystem I2016

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

      J. Photochem. Photobiol. B: Biology

      Volume: 160 Pages: 364-375

    • DOI

      10.1016/j.jphotobiol.2016.04.009

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Four-Electron Model for Singlet and Triplet Excitation Energy Transfers with Inclusion of Coherence Memory, Inelastic Tunneling and Nuclear Quantum Effects2016

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

      Chem. Phys.

      Volume: 474 Pages: 18-24

    • DOI

      10.1016/j.chemphys.2016.05.001

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Local thermodynamics of the water molecules around single- and double-stranded DNA studied by grid inhomogeneous solvation theory2016

    • Author(s)
      Nakano M, Tateishi-Karimata H, Tanaka S, Tama F, Miyashita O, Nakano S, and Sugimoto N
    • Journal Title

      CHEMICAL PHYSICS LETTERS

      Volume: 660 Pages: 250-255

    • DOI

      10.1016/j.cplett.2016.08.032

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Meteorite Impact-Induced Rapid NH3 Production on Early Earth: Ab Initio Molecular Dynamics Simulation2016

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

      Sci. Rep.

      Volume: 6 Issue: 1 Pages: 38953-38953

    • DOI

      10.1038/srep38953

    • NAID

      120005950966

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Correlational and Thermodynamic Properties of Finite-Temperature Electron Liquids in the Hypernetted-Chain Approximation2016

    • Author(s)
      S. Tanaka
    • Journal Title

      J. Chem. Phys.

      Volume: 145 Issue: 21 Pages: 214104-214104

    • DOI

      10.1063/1.4969071

    • NAID

      120005970764

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking2016

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

      Molecules

      Volume: 21 Issue: 11 Pages: 1604-1604

    • DOI

      10.3390/molecules21111604

    • NAID

      120005950958

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Effects of Bridge Functions on Radial Distribution Functions of Liquid Water2015

    • Author(s)
      S. Tanaka, M. Nakano
    • Journal Title

      Interdiscip. Sci. Comput. Life Sci.

      Volume: 7 Issue: 2 Pages: 152-156

    • DOI

      10.1007/s12539-015-0013-2

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Systems Approach to Excitation-Energy and Electron Transfer Reaction Networks in Photosystem II Complex: Model Studies for Chlorophyll a Fluorescence Induction Kinetics2015

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

      J. Theor. Biol.

      Volume: 380 Pages: 220-237

    • DOI

      10.1016/j.jtbi.2015.05.006

    • Related Report
      2015 Research-status Report
    • Peer Reviewed
  • [Journal Article] Protein-Ligand Docking Using Fitness Learning-Based Artificial Bee Colony with Proximity Stimuli2015

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

      Phys. Chem. Chem. Phys.

      Volume: 17 Issue: 25 Pages: 16412-16417

    • DOI

      10.1039/c5cp01394a

    • Related Report
      2015 Research-status Report
    • Peer Reviewed
  • [Journal Article] Thermodynamic Properties of Water Molecules in the Presence of Cosolute Depend on DNA Structure: A Study Using Grid Inhomogeneous Solvation Theory2015

    • Author(s)
      M. Nakano, H. Tateishi-Karimata, S. Tanaka, F. Tama, O. Miyashita, S. Nakano, N. Sugimoto
    • Journal Title

      Nucl. Acids Res.

      Volume: 43 Pages: 10114-10125

    • DOI

      10.1093/nar/gkv1133

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Theoretical prediction and experimental verification on enantioselectivity of haloacid dehalogenase L-DEX YL with chloropropionate2015

    • Author(s)
      Hirotaka Kondo, Kazuhiro J. Fujimoto, Shigenori Tanaka, Hiroyuki Deki, and Takashi Nakamura
    • Journal Title

      Chem. Phys. Lett.

      Volume: 623 Pages: 101-107

    • DOI

      10.1016/j.cplett.2015.01.053

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Novel Type of Virtual Ligand Screening on the Basis of Quantum-Chemical Calculations for Protein-Ligand Complexes and Extended Clustering Techniques2015

    • Author(s)
      R. Kurauchi, C. Watanabe, K. Fukuzawa, S. Tanaka
    • Journal Title

      Comput. Theor. Chem.

      Volume: 1061 Pages: 12-22

    • DOI

      10.1016/j.comptc.2015.02.016

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] i-Motifs Are More Stable than G-Quadruplexes in a Hydrated Ionic Liquid2015

    • Author(s)
      H. Tateishi-Karimata, M. Nakano, S. Pramanik, S. Tanaka, N. Sugimoto
    • Journal Title

      Chem. Commun.

      Volume: 51 Issue: 32 Pages: 6909-6912

    • DOI

      10.1039/c5cc00666j

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Explicit Solvation Modulates Intra- and Inter-Molecular Interactions within DNA: Electronic Aspects Revealed by the Ab Initio Fragment Molecular Orbital (FMO) Method2015

    • Author(s)
      K. Fukuzawa, I. Kurisaki, C. Watanabe, Y. Okiyama, Y. Mochizuki, S. Tanaka, Y. Komeiji
    • Journal Title

      Comput. Theor. Chem.

      Volume: 1054 Pages: 29-37

    • DOI

      10.1016/j.comptc.2014.11.020

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] The affinity of molecular ions for DNA structures is determined by solvent accessible surface area2014

    • Author(s)
      M. Nakano, H. Tateishi-Karimata, S. Tanaka, and N. Sugimoto
    • Journal Title

      J. Phys. Chem. B

      Volume: 118 Issue: 32 Pages: 9583-9594

    • DOI

      10.1021/jp505107g

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Interaction Energy Analysis on Specific Binding of Influenza Virus Hemagglutinin to Avian and Human Sialosaccharide Receptors: Importance of Mutation-Induced Structural Change2014

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

      J. Mol. Graph. Model.

      Volume: 53 Pages: 48-58

    • DOI

      10.1016/j.jmgm.2014.07.004

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] A Significant Role of Arg41 Residue in the Enzymatic Reaction of Haloacid Dehalogenase L-DEX YL Studied by QM/MM Method2014

    • Author(s)
      H. Kondo, T. Nakamura, S. Tanaka
    • Journal Title

      J. Mol. Catal. B

      Volume: 110 Pages: 23-31

    • DOI

      10.1016/j.molcatb.2014.09.006

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Charge Clamps of Lysines and Hydrogen Bonds Play Key Roles in the Mechanism to Fix Helix 12 in the Agonist and Antagonist Positions of Estrogen Receptor α: Intramolecular Interactions Studied by the Ab Initio Fragment Molecular Orbital Method2014

    • Author(s)
      C. Watanabe, K. Fukuzawa, S. Tanaka, and S. Aida-Hyugaji
    • Journal Title

      J. Phys. Chem

      Volume: B118 Issue: 19 Pages: 4993-5008

    • DOI

      10.1021/jp411627y

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Accuracy of the Fragment Molecular Orbital (FMO) Calculations for DNA: Total Energy, Molecular Orbital, and Inter-Fragment Interaction Energy2014

    • Author(s)
      K. Fukuzawa, C. Watanabe, I. Kurisaki, N. Taguchi, Y. Mochizuki, T. Nakano, S. Tanaka, Y. Komeiji
    • Journal Title

      Computational and Theoretical Chemistry

      Volume: 1034 Pages: 7-16

    • DOI

      10.1016/j.comptc.2014.02.002

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Classical Density Functional Calculation of Radial Distribution Functions of Liquid Water2014

    • Author(s)
      S. Tanaka and M. Nakano
    • Journal Title

      Chem. Phys

      Volume: 430 Pages: 18-22

    • DOI

      10.1016/j.chemphys.2013.12.007

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Hierarchical Coarse-Graining Model for Photosystem II Including Electron and Excitation-Energy Transfer Processes2014

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

      BioSystems

      Volume: 117 Pages: 15-29

    • DOI

      10.1016/j.biosystems.2013.12.008

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Choline Ion Interactions with DNA Atoms Explain Unique Stabilization of A-T Base Pairs in DNA Duplexes: A Microscopic View2014

    • Author(s)
      M. Nakano, H. Tateishi-Karimata, S. Tanaka, N. Sugimoto
    • Journal Title

      J. Phys. Chem. B

      Volume: 118 Issue: 2 Pages: 379-389

    • DOI

      10.1021/jp406647b

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Electron- Correlated Fragment-Molecular-Orbital Calculations for Biomolecular and Nano Systems2014

    • Author(s)
      S. Tanaka, Y. Mochizuki, Y. Komeiji, Y. Okiyama, K. Fukuzawa
    • Journal Title

      Phys. Chem. Chem. Phys

      Volume: 16 Issue: 22 Pages: 10310-10344

    • DOI

      10.1039/c4cp00316k

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [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
    • Place of Presentation
      東京大学山上会館(東京都・文京区)
    • Year and Date
      2017-04-12
    • Related Report
      2016 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」
    • Place of Presentation
      慶応義塾大学(神奈川県・横浜市)
    • Year and Date
      2017-03-16
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] 水和生体分子系の熱力学2017

    • Author(s)
      田中成典
    • Organizer
      公開シンポジウム「気候変動の中での(植物)生態系へのマクロ、ミクロからの考察:光合成、植物進化までを視座に置いて」
    • Place of Presentation
      酪農学園大学(北海道・江別市)
    • Year and Date
      2017-02-20
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] 水溶液中の生体分子の構造変化に伴う自由エネルギー解析2017

    • Author(s)
      田中成典
    • Organizer
      FIBER未来大学・第2回研究成果報告会
    • Place of Presentation
      甲南大学(兵庫県・神戸市)
    • Year and Date
      2017-01-10
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Theoretical Study on Dynamics and Functions of Solvated Biomolecules2016

    • Author(s)
      S. Tanaka
    • Organizer
      FIBER Future College: FIBER国際核酸サミット2016
    • Place of Presentation
      甲南大学(兵庫県・神戸市)
    • Year and Date
      2016-07-06
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 生体分子系のボトムアップ・マルチスケールシミュレーションに向けて2015

    • Author(s)
      田中成典
    • Organizer
      High Performance Computing Chemistry 2015ワークショップ
    • Place of Presentation
      理化学研究所・計算科学研究機構(兵庫県・神戸市)
    • Year and Date
      2015-12-01
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] 生体分子系における非平衡過程2015

    • Author(s)
      田中成典
    • Organizer
      バイオスーパーコンピューティング神戸2015
    • Place of Presentation
      神戸大学(兵庫県・神戸市)
    • Year and Date
      2015-11-30
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] フラグメント分子軌道法に基づくアカデミア創薬2015

    • Author(s)
      田中成典
    • Organizer
      CBI学会2015年大会
    • Place of Presentation
      タワーホール船堀(東京都・江東区)
    • Year and Date
      2015-10-28
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] Nonequilibrium Processes in Biomolecular Systems2015

    • Author(s)
      S. Tanaka
    • Organizer
      Workshop on "Current Topics in Nano Simulations" (CT-NanoSim2015)
    • Place of Presentation
      Tsukuba University (Ibaraki, Tsukuba)
    • Year and Date
      2015-09-17
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] タンパク質の量子化学計算の現状2015

    • Author(s)
      田中成典
    • Organizer
      第15回日本蛋白質科学会年会
    • Place of Presentation
      あわぎんホール(徳島県・徳島市)
    • Year and Date
      2015-06-24
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] Toward First-Principles Simulations for the Origin of Life2015

    • Author(s)
      S. Tanaka
    • Organizer
      Mini-Symposium on Functional and Biogenous Materials II
    • Place of Presentation
      岡山大学(岡山県岡山市)
    • Year and Date
      2015-03-20
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] FMO Pharmaceutical Applications2015

    • Author(s)
      S. Tanaka
    • Organizer
      Workshop on Innovation and Pioneering Technology – Innovation by Synergy of Computational & Synchrotron Radiation Sciences (WINTech 2015)
    • Place of Presentation
      神戸大学(兵庫県神戸市)
    • Year and Date
      2015-03-12
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] 生体分子ダイナミクスにおける階層性と粗視化2015

    • Author(s)
      田中成典
    • Organizer
      神戸大学先端融合科学シンポジウム「生体分子のダイナミクスを眺める」
    • Place of Presentation
      神戸大学(兵庫県神戸市)
    • Year and Date
      2015-01-20
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] 大規模シミュレーションによる生体分子機能デザインの試み2015

    • Author(s)
      田中成典
    • Organizer
      甲南大学先端生命工学研究所(FIBER)私立大学研究基盤形成支援事業第1回研究成果報告会(FIBER未来大学シリーズ Series 10)
    • Place of Presentation
      甲南大学(兵庫県神戸市)
    • Year and Date
      2015-01-07
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] 大規模分子シミュレーション技術の医療・創薬への応用2014

    • Author(s)
      田中成典
    • Organizer
      探索医療薬物研究会第2回合同シンポジウム「創薬と医療-基礎と臨床の架け橋」
    • Place of Presentation
      大阪薬科大学(大阪府高槻市)
    • Year and Date
      2014-09-13
    • Related Report
      2014 Research-status Report
    • Invited
  • [Book] Recent Progress in Quantum Monte Carlo (ACS Symposium Series 1234)2016

    • Author(s)
      S. Tanaka, P.-N. Roy, L. Mitas
    • Total Pages
      173
    • Publisher
      American Chemical Society
    • Related Report
      2016 Annual Research Report
  • [Remarks] Research by Shigenori Tanaka

    • URL

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

    • Related Report
      2016 Annual Research Report
  • [Remarks] FMO創薬コンソーシアム

    • URL

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

    • Related Report
      2016 Annual Research Report
  • [Remarks] 神戸大学計算科学教育センター 遠隔講義「計算生命科学の基礎III」

    • URL

      http://www.eccse.kobe-u.ac.jp/distance_learning/

    • Related Report
      2016 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計算生物学講座

    • URL

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

    • Related Report
      2015 Research-status Report 2014 Research-status Report
  • [Remarks] FMO創薬コンソーシアム

    • URL

      http://eniac.scitec.kobe-u.ac.jp/fmodd/index.html

    • Related Report
      2015 Research-status Report
  • [Remarks] 神戸大学計算科学教育センター 遠隔講義「計算生命科学の基礎」

    • URL

      http://www.eccse.kobe-u.ac.jp/distance_learning/

    • Related Report
      2015 Research-status Report

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Published: 2014-04-04   Modified: 2018-03-22  

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