• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

Three-dimensional data mining from protein molecular surfaces for discovery of knowledge about protein functions

Research Project

Project/Area Number 24300056
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypePartial Multi-year Fund
Section一般
Research Field Intelligent informatics
Research InstitutionKobe University

Principal Investigator

OHKAWA Takenao  神戸大学, 大学院システム情報学研究科, 教授 (30223738)

Project Period (FY) 2012-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥17,550,000 (Direct Cost: ¥13,500,000、Indirect Cost: ¥4,050,000)
Fiscal Year 2016: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2015: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Fiscal Year 2014: ¥8,580,000 (Direct Cost: ¥6,600,000、Indirect Cost: ¥1,980,000)
Fiscal Year 2013: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
Fiscal Year 2012: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Keywords知識発見 / データマイニング / バイオインフォマティクス / 三次元データ / バイオデータ処理 / バイクラスタリング
Outline of Final Research Achievements

In this research, we aimed to develop several methods of three-dimensional data mining from protein molecular surfaces for discovery of knowledge about protein functions. Molecular surfaces are regarded as three-dimensional images that are expressed by point clouds or graphs. The functional sites of proteins are extracted by biclustering of matched points in the point clouds or by an optimal graph discovery. In addition, we proposed an effective method to search for related articles on protein structure analysis by considering a user's intention and developed a new method for the automatic extraction of protein-protein interaction information from scientific articles by predicting dominant keywords.

Report

(6 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • Research Products

    (25 results)

All 2016 2015 2014 2013 2012

All Journal Article (9 results) (of which Peer Reviewed: 9 results,  Open Access: 3 results,  Acknowledgement Compliant: 5 results) Presentation (16 results) (of which Int'l Joint Research: 3 results)

  • [Journal Article] Protein-protein Interaction Extraction with Feature Selection by Evaluating Contribution Levels of Groups Consisting of Related Features2016

    • Author(s)
      Phan Thi Thanh Thuy and Takenao Ohkawa
    • Journal Title

      BMC Bioinformatics

      Volume: Vol. 17, Suppl. 7 Issue: S7 Pages: 517-531

    • DOI

      10.1186/s12859-016-1100-z

    • Related Report
      2016 Annual Research Report 2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] A Method of Searching for Related Literature on Protein Structure Analysis by Considering a User's Intention2015

    • Author(s)
      Azusa Ito and Takenao Ohkawa
    • Journal Title

      BMC Bioinformatics

      Volume: Vol. 16, Suppl. 7 Issue: S7

    • DOI

      10.1186/1471-2105-16-s7-s4

    • Related Report
      2015 Annual Research Report 2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Extraction of Protein-Protein Interaction from Scientific Articles by Predicting Dominant Keywords2015

    • Author(s)
      Shun Koyabu, Thi Thanh Thuy Phan, and Takenao Ohkawa
    • Journal Title

      BioMed Research International

      Volume: 2015 Pages: 1-13

    • DOI

      10.1155/2015/928531

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] A Method of Retrieving Articles on Protein Structure Analysis from Query Articles Using a Concept Graph2015

    • Author(s)
      伊藤 あずさ, 大川 剛直
    • Journal Title

      IEEJ Transactions on Electronics, Information and Systems

      Volume: 135 Issue: 3 Pages: 340-348

    • DOI

      10.1541/ieejeiss.135.340

    • NAID

      130004870151

    • ISSN
      0385-4221, 1348-8155
    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Binding Site Extraction by Similar Subgraphs Mining from Protein Molecular Surfaces and Its Application to Protein Classification2014

    • Author(s)
      Natsumi Kurumatani, Hiroyuki Monji, and Takenao Ohkawa
    • Journal Title

      International Journal on Artificial Intelligence Tools

      Volume: Vol. 23, No. 3 Issue: 03 Pages: 1460007-1460007

    • DOI

      10.1142/s0218213014600070

    • Related Report
      2014 Annual Research Report 2013 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Binding Site Extraction by Detecting Optimal Graphs from Protein Molecular Surfaces2014

    • Author(s)
      Takuma Mitsui and Takenao Ohkawa
    • Journal Title

      International Journal of Bioscience, Biochemistry and Bioinformatics

      Volume: Vol. 4, No. 1 Pages: 28-32

    • DOI

      10.7763/ijbbb.2014.v4.305

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Method of Extracting Sentences Containing Protein Function Information from Articles by Iterative Learning with Feature Update2013

    • Author(s)
      Kazunori Miyanishi and Takenao Ohkawa
    • Journal Title

      Lecture Notes in Bioinformatics

      Volume: Vol. 7845 Pages: 81-94

    • DOI

      10.1007/978-3-642-38342-7_8

    • ISBN
      9783642383410, 9783642383427
    • Related Report
      2013 Annual Research Report 2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Predicting Toxicity of Food-Related Compounds Using Fuzzy Decision Trees2013

    • Author(s)
      Yajima, D., Ohkawa, T., Muroi, K., Imaishi, H.
    • Journal Title

      International Journal of Bioscience, Biochemistry and Bioinformatics

      Volume: 4 Pages: 33-38

    • DOI

      10.7763/ijbbb.2014.v4.306

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Method of Retrieving Articles on Protein Structure Analysis from User Intention2013

    • Author(s)
      Tomoki Aso and Takenao Ohkawa
    • Journal Title

      International Journal of Bioscience, Biochemistry and Bioinformatics

      Volume: Vol. 3, No. 3 Pages: 182-186

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Presentation] Optimal Graph Detection with Summary Graph for Identification of Ligand-Binding Site from Protein Molecular Surface2016

    • Author(s)
      Masaya Yatori, Takuma Mitsui, and Takenao Ohkawa
    • Organizer
      Biotechnology and Bioinformatics Symposium 2016
    • Place of Presentation
      Provo, Utah (USA)
    • Year and Date
      2016-12-08
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Extraction of Protein Recognition Spots by Biclustering Considering Exclusive Selection of Column2016

    • Author(s)
      Hiroto Nishimura, Kento Sakaue, and Takenao Ohkawa
    • Organizer
      Biotechnology and Bioinformatics Symposium 2016
    • Place of Presentation
      Provo, Utah (USA)
    • Year and Date
      2016-12-08
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Protein-protein Interaction Extraction from Literature with Evaluation of Cross-corpus Learning2016

    • Author(s)
      Thi Thanh Thuy Phan, Takenao Ohkawa, and AkihitoYamamoto
    • Organizer
      人工知能学会第101回人工知能基本問題研究会(SIG-FPAI)
    • Place of Presentation
      北海道大学(北海道・札幌市)
    • Year and Date
      2016-08-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] 最適グラフ発見に基づく蛋白質表面からの結合部位抽出におけるグラフの抽象化2016

    • Author(s)
      八鳥真弥,三井拓真,大川剛直
    • Organizer
      第108回MPS・第46回BIO合同研究発表会
    • Place of Presentation
      沖縄科学技術大学院大学(沖縄県・国頭郡恩納村)
    • Year and Date
      2016-07-04
    • Related Report
      2016 Annual Research Report
  • [Presentation] 蛋白質分子表面マッチングと項目集合からの排他的選択を考慮したバイクラスタリングを用いた重要特徴点抽出2016

    • Author(s)
      西村宏人,阪上絢人,大川剛直
    • Organizer
      第108回MPS・第46回BIO合同研究発表会
    • Place of Presentation
      沖縄科学技術大学院大学(沖縄県・国頭郡恩納村)
    • Year and Date
      2016-07-04
    • Related Report
      2016 Annual Research Report
  • [Presentation] Protein-protein Interaction Extraction with Feature Selection by Evaluating Contribution Levels of Groups Consisting of Related Features2015

    • Author(s)
      Phan Thi Thanh Thuy and Takenao Ohkawa
    • Organizer
      Biotechnology and Bioinformatics Symposium 2015
    • Place of Presentation
      Provo, Utah (USA)
    • Year and Date
      2015-12-10
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] A Method of Searching for Related Literature on Protein Structure Analysis by Considering a User's Intention2014

    • Author(s)
      Azusa Ito and Takenao Ohkawa
    • Organizer
      Biotechnology and Bioinformatics Symposium 2014
    • Place of Presentation
      Provo, Utah (USA)
    • Year and Date
      2014-12-11 – 2014-12-12
    • Related Report
      2014 Annual Research Report
  • [Presentation] 概念階層グラフを利用した検索意図の反映が可能な蛋白質構造解析関連文献検索手法2014

    • Author(s)
      伊藤 あずさ, 大川 剛直
    • Organizer
      電気学会 第58回情報システム研究会
    • Place of Presentation
      電気学会会議室 (東京都)
    • Year and Date
      2014-05-16
    • Related Report
      2014 Annual Research Report
  • [Presentation] Binding Site Extraction by Detecting Optimal Graphs from Protein Molecular Surfaces2013

    • Author(s)
      Takuma Mitsui and Takenao Ohkawa
    • Organizer
      2013 3rd Journal Conference on Bioscience, Biochemistry and Bioinformatics
    • Place of Presentation
      Paris, France
    • Related Report
      2013 Annual Research Report
  • [Presentation] Predicting Toxicity of Food-Related Compounds Using Fuzzy Decision Trees2013

    • Author(s)
      Daishi Yajima, Takenao Ohkawa, Kouhei Muroi, and Hiromasa Imaishi
    • Organizer
      2013 3rd Journal Conference on Bioscience, Biochemistry and Bioinformatics
    • Place of Presentation
      Paris, France
    • Related Report
      2013 Annual Research Report
  • [Presentation] Super-resolved 3D Reconstruction for Parking Assistance Using Projective Transformation2013

    • Author(s)
      Keiko Nakajima, Takenao Ohkawa, Shiho Tanaka, and Toshio Ito
    • Organizer
      19th Korea-Japan Workshop on Frontiers of Computer Vision
    • Place of Presentation
      Incheon, Korea
    • Related Report
      2012 Annual Research Report
  • [Presentation] Method of Extracting Sentences About Protein Interaction from the Literature on Protein Structure Analysis Using Selective Transfer Learning2012

    • Author(s)
      Shun Koyabu, Riku Kyougoku, and Takenao Ohkawa
    • Organizer
      IEEE 12th International Conference on Bioinformatics and Bioengineering
    • Place of Presentation
      Larnaca, Cyprus
    • Related Report
      2012 Annual Research Report
  • [Presentation] Binding Site Extraction by Similar Subgraphs Mining from Protein Molecular Surfaces2012

    • Author(s)
      Natsumi Kurumatani, Hiroyuki Monii, and Takenao Ohkawa
    • Organizer
      IEEE 12th International Conference on Bioinformatics and Bioengineering
    • Place of Presentation
      Larnaca, Cyprus
    • Related Report
      2012 Annual Research Report
  • [Presentation] 3次元画像特徴量を用いた蛋白質分子表面比較2012

    • Author(s)
      車谷奈都実, 大川剛直
    • Organizer
      情報処理学会第29回バイオ情報学研究会
    • Place of Presentation
      沖縄科学技術大学院大学
    • Related Report
      2012 Annual Research Report
  • [Presentation] 複数の分類器に基づく半教師あり学習を用いた文献からの蛋白質間相互作用抽出2012

    • Author(s)
      小薮駿, 大川剛直
    • Organizer
      情報処理学会第29回バイオ情報学研究会
    • Place of Presentation
      沖縄科学技術大学院大学
    • Related Report
      2012 Annual Research Report
  • [Presentation] A Method of Extracting Sentences Containing Protein Function Information from Articles b Iterative Learning with Feature Update2012

    • Author(s)
      Kazunori Miyanishi and Takenao Ohkawa
    • Organizer
      9th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics
    • Place of Presentation
      Houston, Texas, USA
    • Related Report
      2012 Annual Research Report

URL: 

Published: 2012-04-24   Modified: 2019-07-29  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi