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Development of new simulation methods at the molecular layer

Planned Research

Project AreaEstablishment of Integrative Multi-level Systems Biology and its Applications
Project/Area Number 22136005
Research Category

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

Allocation TypeSingle-year Grants
Review Section Complex systems
Research InstitutionTohoku University

Principal Investigator

KENGO Kinoshita  東北大学, 情報科学研究科, 教授 (60332293)

Project Period (FY) 2010-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥62,660,000 (Direct Cost: ¥48,200,000、Indirect Cost: ¥14,460,000)
Fiscal Year 2014: ¥9,620,000 (Direct Cost: ¥7,400,000、Indirect Cost: ¥2,220,000)
Fiscal Year 2013: ¥10,140,000 (Direct Cost: ¥7,800,000、Indirect Cost: ¥2,340,000)
Fiscal Year 2012: ¥10,660,000 (Direct Cost: ¥8,200,000、Indirect Cost: ¥2,460,000)
Fiscal Year 2011: ¥10,530,000 (Direct Cost: ¥8,100,000、Indirect Cost: ¥2,430,000)
Fiscal Year 2010: ¥21,710,000 (Direct Cost: ¥16,700,000、Indirect Cost: ¥5,010,000)
Keywordsイオンチャネル / 構造モデリング / 分子動力学法 / 多階層シミュレーション / 生命情報科学 / 膜タンパク質 / ブラウニアン動力学
Outline of Final Research Achievements

Systems-biology approaches often suffer from the description of molecular details, because atomic details are too much to be considered with whole systems at the same time. As a result, it becomes hard to consider molecular interactions with drugs and to evaluate the effect of genomic variations due to the individual differences. To overcome the difficulty, we have developed a few methods to consider the interaction between molecular level and an upper level of the different biological layers. More specifically, we develop a method of model building for channel proteins, a method to analyze long-time molecular dynamics simulation results, and a method to simulate the mutant proteins to evaluate the molecular function differences.

Report

(6 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (33 results)

All 2015 2014 2013 2012 2011 2010 Other

All Journal Article (12 results) (of which Peer Reviewed: 12 results,  Open Access: 2 results,  Acknowledgement Compliant: 1 results) Presentation (15 results) (of which Invited: 8 results) Book (5 results) Remarks (1 results)

  • [Journal Article] Okamura Y, Aoki Y, Obayashi T, Tadaka S, Ito S1, Narise T, Kinoshita K.2015

    • Author(s)
      Okamura Y, Aoki Y, Obayashi T, Tadaka S, Ito S1, Narise T, Kinoshita K.
    • Journal Title

      Nucleic Acid Res

      Volume: 43 Issue: D1 Pages: D82-D86

    • DOI

      10.1093/nar/gku1163

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Blind prediction of interfacial water positions in CAPRI2014

    • Author(s)
      Lensink MF, et al
    • Journal Title

      Proteins

      Volume: 82 Issue: 4 Pages: 620-632

    • DOI

      10.1002/prot.24439

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes2014

    • Author(s)
      Kasahara K and Kinoshita K
    • Journal Title

      BMC Bioinformatics

      Volume: 15 Issue: 1 Pages: 12-12

    • DOI

      10.1186/1471-2105-15-12

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] ATTED-II in 2014: Evaluation of Gene Coexpression in Agriculturally Important Plants2013

    • Author(s)
      Takeshi Obayashi, Yasunobu Okamura, Satoshi Ito, Shu Tadaka, Yuichi Aoki, Matsuyuki Shirota and Kengo Kinoshita
    • Journal Title

      Plant Cell Physiology

      Volume: 55 Issue: 1 Pages: e6-e6

    • DOI

      10.1093/pcp/pct178

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Comprehensive classification and diversity assessment of atomic contacts in protein-small ligand interactions2013

    • Author(s)
      Kasahara K
    • Journal Title

      J Chem Inf Model

      Volume: 53 Issue: 1 Pages: 241-248

    • DOI

      10.1021/ci300377f

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Ion concentration-dependent ion conduction mechanism of a voltage-sensitive potassium channel2013

    • Author(s)
      Kasahara K
    • Journal Title

      PLoS One

      Volume: 8 Issue: 2 Pages: e56342-e56342

    • DOI

      10.1371/journal.pone.0056342

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dynamic features of homodimer interfaces calculated by normal-mode analysis2012

    • Author(s)
      Tsuchiya Y
    • Journal Title

      Protein Science

      Volume: 21 Issue: 10 Pages: 1503-1513

    • DOI

      10.1002/pro.2140

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Community-wide assessment of protein-interface modeling suggests improvements to design methodology2011

    • Author(s)
      SJ Fleishman, TA Whitehead, EM Strauch, JE Com, S Qin, HX Zhou, JC Mitchell, ON Demerdash, M Takeda-Shitaka, G Terashi, IH Moal, X Li, PA Bates, M Zacharias, H Park, JS Ko, H Lee, C Seok, T Bourquard, J Bernauer, A Poupon, J Aze, S Soner, SK Ovali, P Ozbek, NB Tal, T Haliloglu, H Hwang, T Vreven, BG Pierce, Z Weng, L Perez-Cano, C Pons, J Fernandez-Recio, F Jiang, F Yang, X Gong, L Cao, X Xu, B Liu, P Wang, C Li, C Wang, CH Robert, M Guharoy, S Liu, Y Huang, L Li, D Guo, Y Chen, Y Xiao, N London, Z Itzhaki, O Schucler-Furman, Y Inbar, V Potapov, M Cohen, G Schreiber, Y Tsuchiya, E Kanamori, DM Standley, H Nakamura, K Kinoshita, CM Driggers, RG Hall, JL Morgan, VL Hsu, J Zhan, Y Yang, Y Zhou, PL Kastritis, AM Bonvin, W Zhang, CJ Camacho, KP Kilambi, A Sircar, JJ Gray, M Ohue, N Uchikoga, Y Matsuzaki, T Ishida, Y Akiyama, R Khashan, S Bush, D Fouches, A Tropsha, J Esquivel-Rodriguez, D Kihara, PB Stranges, R Jacak, B Kuhlman, SY Huang, X Zou, SJ Wodak, J Janin, D Baker
    • Journal Title

      Journal of Molecular Biology

      Volume: volume414 Pages: 289-382

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Assessing the utility of gene co-expression stability in combination with correlation in the analysis of protein-protein interaction networks2011

    • Author(s)
      A Patil, K Nakai, K Kinoshita
    • Journal Title

      BMC genomics

      Volume: 12 Issue: Suppl 3 Pages: S19-S19

    • DOI

      10.1186/1471-2164-12-s3-s19

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Absolute quality evaluation of protein model structures using statistical potentials with respect to the native and reference states2011

    • Author(s)
      M Shirota, T Ishida, K Kinoshita
    • Journal Title

      Proteins

      Volume: 79 Issue: 5 Pages: 1550-1563

    • DOI

      10.1002/prot.22982

    • Related Report
      2011 Annual Research Report 2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] COXPRESdb : a database to compare gene coexpression in seven model animals2011

    • Author(s)
      T Obayashi, K Kinoshita
    • Journal Title

      Nucleic Acids Res

      Volume: 39

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Ligand-binding site prediction of proteins based on known fragment-fragment interactions2010

    • Author(s)
      K Kasahara, K Kinoshita, T Takagi
    • Journal Title

      Bioinformatics

      Volume: 26 Pages: 1493-1499

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] ゲノム情報解析の現状と課題2014

    • Author(s)
      木下賢吾
    • Organizer
      次世代PGSフォーラム設立記念シンポジウム
    • Place of Presentation
      品川プリンスホテル
    • Year and Date
      2014-12-04
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] タンパク質機能解析に向けた立体構造情報の活用基盤の構築2014

    • Author(s)
      木下賢吾
    • Organizer
      第52回日本生物物理学会
    • Place of Presentation
      札幌コンベンションセンター
    • Year and Date
      2014-09-25 – 2014-09-27
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Analysis of the ion permeation mechanism of Kv1.2 using the molecular dynamics simulations of a single point mutant2014

    • Author(s)
      近藤寛子,城田松之,笠原浩太,齊藤俊幸,木下賢吾
    • Organizer
      第52回日本生物物理学会
    • Place of Presentation
      札幌コンベンションセンター
    • Year and Date
      2014-09-25 – 2014-09-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] ゲノム解析による個別化予防に向けた情報科学の挑戦2014

    • Author(s)
      木下賢吾
    • Organizer
      生体医工学大会
    • Place of Presentation
      仙台国際センター
    • Year and Date
      2014-06-24 – 2014-06-26
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 大規模ゲノム解析研究に必要なスパコン環境の構築2014

    • Author(s)
      木下賢吾
    • Organizer
      バイオスーパーコンピューティング東北
    • Place of Presentation
      東北大学
    • Year and Date
      2014-06-02
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Development of descriptors of protein-ligand binding sites with genetic algorithm2013

    • Author(s)
      Kohei Nakamura, Kasahara Kota, Matsuyuki Shirota, Kengo Kinoshita
    • Organizer
      第2回 生命医薬情報学連合大会
    • Place of Presentation
      東京
    • Related Report
      2013 Annual Research Report
  • [Presentation] 蛋白質低分子結合部位の予測に向けた結合部位多様性の解析2012

    • Author(s)
      木下賢吾
    • Organizer
      化学工学会第44回秋季大会
    • Place of Presentation
      仙台
    • Year and Date
      2012-09-21
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] K+チャネルにおける溶液イオン濃度依存なイオン透過機構スイッチングに関する分子動力学的解析2012

    • Author(s)
      笠原浩太
    • Organizer
      蛋白質科学会
    • Place of Presentation
      名古屋国際会議場
    • Year and Date
      2012-06-21
    • Related Report
      2012 Annual Research Report
  • [Presentation] Kota Kasahara, Matsuyuki Shirota, Kengo Kinoshita, GIANT: a web-based application for analyzing three-dimensional structure data of protein-ligand complexes2012

    • Author(s)
      Kasahara K
    • Organizer
      JUCP-III
    • Place of Presentation
      東京
    • Year and Date
      2012-06-07
    • Related Report
      2012 Annual Research Report
  • [Presentation] 次世代生命科学研究に必要な計算機インフラについて2012

    • Author(s)
      木下賢吾
    • Organizer
      データ駆動型生命情報科学の挑戦
    • Place of Presentation
      仙台
    • Year and Date
      2012-05-10
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Seeing in silico is believing, Brief introduction and some recent topics in bioinformatics2011

    • Author(s)
      K Kinoshita
    • Organizer
      The 12^<th>, RIES-Hokudai International Symposium
    • Place of Presentation
      Chateraise Gateaux Kingdom Sapporo(招待講演)
    • Year and Date
      2011-11-22
    • Related Report
      2011 Annual Research Report
  • [Presentation] Illuminating the background and capabilities of statistical potentials of protein structures2011

    • Author(s)
      M Shirota, K Kinoshita
    • Organizer
      The 11th KIAS Conference on Protein Structure and Function
    • Place of Presentation
      Korea Institute for Advanced Study, Seoul, Korea(招待講演)
    • Year and Date
      2011-10-08
    • Related Report
      2011 Annual Research Report
  • [Presentation] Behavior of potassium ions around the potassium channel in relation to permeation events

    • Author(s)
      Toshiyuki Saito, Kota Kasahara, Matsuyuki Shirota, Hiroko Kondo, Kengo Kinoshita
    • Organizer
      生物物理学会
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] In-Silico Approach to Predict the Biological and Biochemical Functions of Uncharacterized Genes.

    • Author(s)
      Kengo Kinoshita
    • Organizer
      NIH-Tohoku University-JSPS Symposium
    • Place of Presentation
      宮城
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 生命科学ビッグデータへの情報科学の挑戦

    • Author(s)
      木下賢吾
    • Organizer
      東北大学電気・情報東京フォーラム2013
    • Place of Presentation
      東京
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Book] 計算科学4巻計算と生命2012

    • Author(s)
      木下賢吾
    • Publisher
      岩波書店
    • Related Report
      2012 Annual Research Report
  • [Book] トランスポートソームの世界2011

    • Author(s)
      木下賢吾(金井好克、竹島浩、森泰生、久保義弘編)
    • Publisher
      京都廣川書店
    • Related Report
      2011 Annual Research Report
  • [Book] Protein function prediction for omics era (chapter 11)2011

    • Author(s)
      K Kinoshita, T Obayashi
    • Publisher
      Springer Verlag
    • Related Report
      2010 Annual Research Report
  • [Book] COXPRESdb:共発現データに基づいた機能関連遺伝子の探索(遺伝子医学MOOK)2011

    • Author(s)
      大林武、木下賢吾
    • Publisher
      メディカルドゥ
    • Related Report
      2010 Annual Research Report
  • [Book] タンパク質の立体構造入門(基礎から構造バイオインフォマティクスヘ)4章と6.3(節藤博幸編)2010

    • Author(s)
      木下賢吾
    • Publisher
      講談社
    • Related Report
      2010 Annual Research Report
  • [Remarks] GIANT

    • URL

      https://giant.hgc.jp/

    • Related Report
      2013 Annual Research Report

URL: 

Published: 2010-08-23   Modified: 2019-07-29  

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