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New Methods for Designing Chemical Structures Using Graph Theory and Kernel Methods

Research Project

Project/Area Number 19200022
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Bioinformatics/Life informatics
Research InstitutionKyoto University

Principal Investigator

AKUTSU Tatsuya  Kyoto University, 化学研究所, 教授 (90261859)

Co-Investigator(Kenkyū-buntansha) KAWABATA Takeo  京都大学, 化学研究所, 教授 (50214680)
HAYASHIDA Morihiro  京都大学, 化学研究所, 助教 (40402929)
NAGAMOCHI Hiroshi  京都大学, 情報学研究科, 教授 (70202231)
Project Period (FY) 2007 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥34,710,000 (Direct Cost: ¥26,700,000、Indirect Cost: ¥8,010,000)
Fiscal Year 2009: ¥12,090,000 (Direct Cost: ¥9,300,000、Indirect Cost: ¥2,790,000)
Fiscal Year 2008: ¥13,000,000 (Direct Cost: ¥10,000,000、Indirect Cost: ¥3,000,000)
Fiscal Year 2007: ¥9,620,000 (Direct Cost: ¥7,400,000、Indirect Cost: ¥2,220,000)
Keywordsカーネル法 / グラフアルゴリズム / 特徴ベクトル / サポートベクターマシン / 列挙アルゴリズム / 動的計画法 / ケモインフォマティクス / グラフ理論 / RNA二次構造 / タンパク質立体構造 / 化学構造 / 立体異性体 / 木構造 / 外平面的グラフ / 構造活性相関 / 光学異性体 / 外平面グラフ
Research Abstract

In this project, we studied a new approach for design of novel chemical compounds by combining graph theory and kernel methods. We developed branch-and-bound algorithms for enumerating tree-like chemical structures from a given feature vector consisting of frequency of labeled paths, dynamic programming-based algorithms for enumerating stereoisomers from a given tree-like or outer-planar chemical structure, and kernel functions that can discriminate stereoisomers. Some of these algorithms were implemented in a newly developed web server.

Report

(5 results)
  • 2009 Annual Research Report   Self-evaluation Report ( PDF )   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • 2007 Annual Research Report
  • Research Products

    (46 results)

All 2010 2009 2008 2007 Other

All Journal Article (23 results) (of which Peer Reviewed: 11 results) Presentation (20 results) Remarks (3 results)

  • [Journal Article] Branch-and-bound algorithms forenumerating treelike chemical graphswith given path frequency usingdetachment-cut2010

    • Author(s)
      Y.Ishida, Y.Kato, L.Zhao, H.Nagamochi, T.Akutsu
    • Journal Title

      Journal of ChemicalInformation and Modeling 50

      Pages: 934-946

    • Related Report
      2009 Final Research Report
  • [Journal Article] Cascleave : towards more accurate prediction of caspase substrate cleavage sites2010

    • Author(s)
      J.Song, H.Tan, H.Shen, K.Mahmood, S.E.Boyd, G.I.Webb, T.Akutsu, J.C.Whisstock
    • Journal Title

      Bioinfornatics 26

      Pages: 752-760

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Branch-and-bound algorithms for enumerating treelike chemical graphs with given path frequency using detachment-cut2010

    • Author(s)
      Y.Ishisa, Y.Kato, L.Zhao, H.Nagamochi, T.Akutsu
    • Journal Title

      Journal of Chemical Information and Modeling 50(採録決定)

      Pages: 834-946

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Enumerating stereoisomers oftree structured molecules usingdynamic programming2009

    • Author(s)
      T.Imada, S.Ota, H.Nagamochi, T.Akutsu
    • Journal Title

      Lecture Notes inComputer Science 5878

      Pages: 14-23

    • Related Report
      2009 Final Research Report
  • [Journal Article] Dynamic programming algorithms and grammatical modeling for protein beta-sheet prediction2009

    • Author(s)
      Y.Kato, T.Akutsu, H.Seki
    • Journal Title

      Journal of Computational Biology 16

      Pages: 945-957

    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Journal Article] A grammatical approach to RNA-RNA interaction prediction2009

    • Author(s)
      Y.Kato, T.Akutsu, H.Seki
    • Journal Title

      Pattern Recognition 42

      Pages: 531-538

    • Related Report
      2009 Final Research Report
  • [Journal Article] Axially chiral binaphthyl surrogates with an inner N-H-N hydrogen bond2009

    • Author(s)
      T.Kawabata, C.Jiang, K.Hayashi, K.Tsubaki, T.Yoshimura, S.Majumdar, T.Sasamori, N.Tokitoh
    • Journal Title

      Journal of the American Chemical Society 131

      Pages: 54-55

    • Related Report
      2009 Final Research Report
  • [Journal Article] Enumerating stereoisomers of tree structured molecules using dynamic programming2009

    • Author(s)
      T. Imada, S. Ota, H. Nagamochi, T. Akutsu
    • Journal Title

      Lecture Notes in Computer Science No. 5878

      Pages: 14-23

    • Related Report
      2009 Self-evaluation Report
  • [Journal Article] Prodepth : predict residue depth by support vector regression approach from sequences only2009

    • Author(s)
      J.Song, H.Tan, K.Mamhood, R.H.P Law, A.M.Buckle, G.I.Webb, T.Akutsu, J.C.Whisstock
    • Journal Title

      PLoS ONE 4

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Enumerating stereoisomers of tree structured molecules using dynamic programming2009

    • Author(s)
      T.Imada, S.Ota, H.Nagamochi, T.Akutsu
    • Journal Title

      Lecture Notes in Computer Science 5878

      Pages: 14-23

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Identification of novel DNA repair proteins via primary sequence2009

    • Author(s)
      J. B. Brown, T. Akutsu
    • Journal Title

      BMC Bioinformatics 10

      Pages: 25-25

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Prediction of RNA secondary structure with pseudoknots using integer programming2009

    • Author(s)
      U. Poolsap, Y. Kato, T. Akutsu
    • Journal Title

      BMC Bioinformatics 10

    • NAID

      110006595413

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A grammatical approach to RNA-RNA interaction prediction2009

    • Author(s)
      Y. Kato, T. Akutsu, H. Seki
    • Journal Title

      Pattern Recognition 42

      Pages: 531-538

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Enumerating tree-like chemical graphs with given path frequency2008

    • Author(s)
      H.Fujiwara, J.Wang, L.Zhao, H.Nagamochi, T.Akutsu
    • Journal Title

      Journal of Chemical Information and Modeling 48

      Pages: 1345-1357

    • Related Report
      2009 Final Research Report
  • [Journal Article] A clustering method for analysis of sequence similarity networks of proteins using maximal components of graphs2008

    • Author(s)
      M.Hayashida, T.Akutsu, H.Nagamochi
    • Journal Title

      IPSJ Transactions on Bioinformatics 49-Sig 5

      Pages: 15-24

    • NAID

      110006684906

    • Related Report
      2009 Final Research Report
  • [Journal Article] Enumerating tree-like chemical graphs with given path frequency2008

    • Author(s)
      H. Fujiwara, J. Wang, L. Zhao, H. Nagamochi, T. Akutsu
    • Journal Title

      Journal of Chemical Information and Modeling Vol. 48

      Pages: 1345-1357

    • Related Report
      2009 Self-evaluation Report
  • [Journal Article] A grammatical approach to RNA-RNA interaction prediction2008

    • Author(s)
      Y. Kato, T. Akutsu, H. Seki
    • Journal Title

      Pattern Recognition Vol. 42

      Pages: 531-538

    • Related Report
      2009 Self-evaluation Report
  • [Journal Article] Enumerating tree-like chemical graphs with given path frequency2008

    • Author(s)
      H. Fujiwara, J. Wang, L. Zhao, H. Nagamochi, T. Akutsu
    • Journal Title

      Journal of Chemical Information and Modeling 48

      Pages: 1345-1357

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] HSEpred : predict half-sphere exposure from protein sequences2008

    • Author(s)
      J. Song, H. Tan, K. Takemoto, T. Akutsu
    • Journal Title

      Bioinformatics 24

      Pages: 1489-1497

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A clustering method for analysis of sequence similarity networks of proteins using maximal components of graphs2008

    • Author(s)
      M. Hayashida, T. Akutsu and H. Nagamochi
    • Journal Title

      IPSJ Transactions on Bioinformatics 49-Sig5

      Pages: 15-24

    • NAID

      110006684906

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Catalytic One-Step Process for the Chemo-and Regioselective Acylation of Carbohydrates.2007

    • Author(s)
      T.Kawabata, W.Muramatsu, T.Nishio,T.Shibata, H.Schedel
    • Journal Title

      Journal of the American Chemical Society 129

      Pages: 12890-12895

    • Related Report
      2009 Final Research Report
  • [Journal Article] Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition2007

    • Author(s)
      T. Tamura and T. Akutsu
    • Journal Title

      BMC Bioinformatics 8

      Pages: 466-466

    • NAID

      120004754353

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Branch-and-bound algorithms for enumerating treelike chemical graphs with given path frequency using detachment-cut

    • Author(s)
      Y. Ishida, Y. Kato, L. Zhao, H. Nagamochi, T. Akutsu
    • Journal Title

      Journal of Chemical Information and Modeling (in press)

    • Related Report
      2009 Self-evaluation Report
  • [Presentation] Dynamic programming algorithms for RNA structure prediction with binding sites2010

    • Author(s)
      U.Poolsap, Y.Kato, T.Akutsu
    • Organizer
      Pacific Symposium on Biocomputing 2010(PSB 2010)
    • Place of Presentation
      Fairmont Orchid, Hawaii, USA
    • Year and Date
      2010-01-07
    • Related Report
      2009 Annual Research Report
  • [Presentation] Enumerating stereoisomers of tree structured molecules using dynamic programming2009

    • Author(s)
      T.Imada, S.Ota, H.Nagamochi, T.Akutsu
    • Organizer
      20th International Symposium on Algorithms and Computation
    • Place of Presentation
      Hawaii, USA
    • Year and Date
      2009-12-16
    • Related Report
      2009 Final Research Report
  • [Presentation] Enumerating stereoisomers of tree structured molecules using dynanic programming2009

    • Author(s)
      T.Imada, S.Ota, H.Nagamochi, T.Akutsu
    • Organizer
      20th International Symposium on Algorithms and Computation(ISAAC 2009)
    • Place of Presentation
      Ala Moana Hotel, Hawaii, USA
    • Year and Date
      2009-12-16
    • Related Report
      2009 Annual Research Report
  • [Presentation] 木構造および化学構造に対する特徴ベクトル:埋め込み、検索、構造推定2009

    • Author(s)
      阿久津達也
    • Organizer
      第12回情報論的学習理論ワークショップ
    • Place of Presentation
      九州大学(福岡)
    • Year and Date
      2009-10-20
    • Related Report
      2009 Final Research Report
  • [Presentation] 木構造および化学構造に対する特徴ベクトル : 埋め込み、検索、構造推定2009

    • Author(s)
      阿久津達也
    • Organizer
      第12回情報論的学習理論ワークショップ
    • Place of Presentation
      九州大学
    • Year and Date
      2009-10-20
    • Related Report
      2009 Self-evaluation Report
  • [Presentation] 木構造および化学構造に対する特徴ベクトル : 埋め込み、検索、構造推定2009

    • Author(s)
      阿久津達也
    • Organizer
      第12回情報論的学習理論ワークショップ
    • Place of Presentation
      九州大学医学部 百年講堂
    • Year and Date
      2009-10-20
    • Related Report
      2009 Annual Research Report
  • [Presentation] 化合物に対するカーネル法 : 分類から設計へ2009

    • Author(s)
      阿久津達也
    • Organizer
      第41回 人工知能学会 分子生物情報研究会
    • Place of Presentation
      京都大学 工学部10号館
    • Year and Date
      2009-08-28
    • Related Report
      2009 Annual Research Report
  • [Presentation] Enumeratingcolored and rooted outerplanar graphs,情報処理学会2009

    • Author(s)
      J.Wang, H.Nagamochi
    • Organizer
      第129回アルゴリズム研究会
    • Place of Presentation
      東芝科学館(東京)
    • Year and Date
      2009-03-05
    • Related Report
      2009 Final Research Report
  • [Presentation] Improved algorithms for enumerating tree-like chemical graphs with given path frequency2008

    • Author(s)
      Y.Ishida, L.Zhao, H.Nagamochi, T.Akutsu
    • Organizer
      The 19th Int.Conference on Genome Informatics
    • Place of Presentation
      Gold Coast, Australia
    • Year and Date
      2008-12-01
    • Related Report
      2009 Final Research Report
  • [Presentation] Improved algorithms for enumerating tree-like chemical graphs with given path frequency2008

    • Author(s)
      Y. Ishida, L. Zhao, H. Nagamochi, T. Akutsu
    • Organizer
      The 19th Int. Conference on Genome Informatics
    • Place of Presentation
      Gold Coast, Australia
    • Year and Date
      2008-12-01
    • Related Report
      2009 Self-evaluation Report 2008 Annual Research Report
  • [Presentation] Kernel-based approachs to classification and design of chemical compounds2008

    • Author(s)
      T. Akutsu
    • Organizer
      The 2nd Taiwan-Japan Young Researchers Conferenceon Computational and Systems Biology
    • Place of Presentation
      産業技術総合研究所生命情報工学研究センター
    • Year and Date
      2008-11-05
    • Related Report
      2008 Annual Research Report
  • [Presentation] Prediction of protein beta-sheets : dynamic programming versus grammatical approach2008

    • Author(s)
      Y. Kato, T. Akutsu, H. Seki
    • Organizer
      3rd IAPR International Conference on Pattern Recognition in Bioinformatics
    • Place of Presentation
      Melbourne, Australia
    • Year and Date
      2008-10-15
    • Related Report
      2008 Annual Research Report
  • [Presentation] 化合物に対するカーネル法 -分類から設計へ-2008

    • Author(s)
      阿久津達也
    • Organizer
      人工知能学会第71回人工知能基本問題研究会
    • Place of Presentation
      北海道大学
    • Year and Date
      2008-09-18
    • Related Report
      2008 Annual Research Report
  • [Presentation] 列挙型アルゴリズムのバイオインフォマティクスへの応用2008

    • Author(s)
      阿久津達也
    • Organizer
      第7回情報科学技術フォーラム
    • Place of Presentation
      慶応義塾大学(神奈川)
    • Year and Date
      2008-09-02
    • Related Report
      2009 Final Research Report
  • [Presentation] 列挙型アルゴリズムのバイオインフォマティクスヘの応用2008

    • Author(s)
      阿久津達也
    • Organizer
      第7回情報科学技術フォーラム
    • Place of Presentation
      慶応義塾大学
    • Year and Date
      2008-09-02
    • Related Report
      2008 Annual Research Report
  • [Presentation] Prediction of RNA secondary structure with pseudoknots using integer Drogramming2008

    • Author(s)
      U. Poolsap, Y. Kato, T. Akutsu
    • Organizer
      8th International Workshop on Bioinformatics, Systems Biology
    • Place of Presentation
      Berlin, Germany
    • Year and Date
      2008-06-08
    • Related Report
      2008 Annual Research Report
  • [Presentation] 不斉炭素原子を考慮した化合物に対するグラフカーネル法2008

    • Author(s)
      浦田隆史, J.B.Brown, 田村武幸, 川端猛夫, 阿久津達也
    • Organizer
      情報処理学会バイオ情報学研究会
    • Place of Presentation
      九州大学(福岡)
    • Year and Date
      2008-03-04
    • Related Report
      2009 Final Research Report 2007 Annual Research Report
  • [Presentation] A graph kernel method incorporating chirality2007

    • Author(s)
      T.Urata, J.B.Brown, T. Tamura, T.Kawabata, T. Akutsu
    • Organizer
      日本バイオインフォマティクス学会年会
    • Place of Presentation
      日本未来館(東京)
    • Year and Date
      2007-12-19
    • Related Report
      2009 Final Research Report 2007 Annual Research Report
  • [Presentation] A graph kernel method incorporating chirality2007

    • Author(s)
      T. Urata, J. B. Brown, T. Tamura, T. Kawabata, T. Akutsu
    • Organizer
      日本バイオインフォマティクス学会年会
    • Place of Presentation
      日本未来館 (東京)
    • Year and Date
      2007-12-18
    • Related Report
      2009 Self-evaluation Report
  • [Presentation] An efficient algorithm for generating colored outerplanar graphs2007

    • Author(s)
      W. Jiexun, Z. Liang, H. Nagamochi and T. Akutsu
    • Organizer
      The 4th Annual Conference on Theory and Applications of Models of Computation
    • Place of Presentation
      Shanghai, China
    • Year and Date
      2007-05-25
    • Related Report
      2007 Annual Research Report
  • [Remarks] 木状化合物列挙WEBサーバー

    • URL

      http://sunflower.kuicr.kyoto-u.ac.jp/tools/enumol/index-j.htm

    • Related Report
      2009 Final Research Report
  • [Remarks] 木状化学構造の数え上げサーバー EnuMol

    • URL

      http://sunflower.kuicr.kyoto-u.ac.jp/tools/enumol/

    • Related Report
      2009 Self-evaluation Report
  • [Remarks] 化学構造数え上げサーバEnuMol

    • URL

      http://sunflower.kuicr.kyoto-u.ac.jp/tools/enumol/

    • Related Report
      2009 Annual Research Report

URL: 

Published: 2007-04-01   Modified: 2016-04-21  

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