Fast and Flexible Searching Methods for Protein 3-D Structure Databases and Their Applications

• Project/Area Number: 20700264
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Bioinformatics/Life informatics
• Research Institution: The University of Tokyo
• Principal Investigator: SHIBUYA Tetsuo The University of Tokyo, 医科学研究所, 准教授 (60396893)
• Project Period (FY): 2008 – 2010
• Project Status: Completed (Fiscal Year 2010)
• Budget Amount: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2010: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2009: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2008: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
• Keywords: アルゴリズム / 検索技術 / データベース / 生物情報 / タンパク質 / 3次元立体構造

Research Abstract

We explored research on similarity search algorithms for protein 3-D structure databases, and succeeded in developing various algorithms which must benefit the future structural biology a lot and are highly praised in the international research community. Especially we developed a very fast fundamental linear-time protein 3-D structure database searching algorithm, which is practically and theoretically much faster than any of previous algorithms.

Research Products

• [Journal Article] Linear-Time Protein 3-D Structure Searching with Insertions and Deletions (2010)
  • Author(s): Tetsuo Shibuya, Jesper Jansson, Kunihiko Sadakane
  • Journal Title: BMC Algorithms for Molecular Biology Vol.5 Pages: 7-7
  • Peer Reviewed
• [Journal Article] Geometric Suffix Tree : Indexing Protein 3-D Structures (2010)
  • Author(s): Tetsuo Shibuya
  • Journal Title: Journal of the ACM Vol.57, No.3, Article No.15 Pages: 1-17
  • Peer Reviewed
• [Journal Article] Searching Protein 3-D Structures in Linear Time (2010)
  • Author(s): Tetsuo Shibuya
  • Journal Title: Journal of Computational Biology Vol.17, No.3 Pages: 203-219
  • Peer Reviewed
• [Journal Article] Fast Hinge Detection Algorithms for Flexible Protein Structures (2010)
  • Author(s): Tetsuo Shibuya
  • Journal Title: IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol.7, No.2 Pages: 333-341
  • Peer Reviewed
• [Journal Article] Searching Protein 3-D Structures in Faster Than Linear Time (2010)
  • Author(s): Tetsuo Shibuya
  • Journal Title: Journal of Computational Biology Vol.17, No.4 Pages: 593-602
  • Peer Reviewed
• [Journal Article] Searching Protein 3-D Structures in Faster Than Linear Time (2010)
  • Author(s): Tetsuo Shibuya
  • Journal Title: Journal of Computational Biology Volume: 17(4) Pages: 593-602
  • Peer Reviewed
• [Journal Article] Fast Hinge Detection Algorithms for Flexible Protein Structures (2010)
  • Author(s): Tetsuo Shibuya
  • Journal Title: IEEE/ACM Transactions on Computational Biology and Bioinformatics Volume: 7(2) Pages: 333-341
  • Peer Reviewed
• [Journal Article] Searching Protein 3-D Structures in Linear Time (2010)
  • Author(s): Tetsuo Shibuya
  • Journal Title: Journal of Computational Biology 17(3) Pages: 203-219
  • Peer Reviewed
• [Journal Article] Geometric Suffix Tree : Indexing Protein 3-D Structures (2010)
  • Author(s): Tetsuo Shibuya
  • Journal Title: Journal of the ACM 57(3)
  • Peer Reviewed
• [Journal Article] Linear-Time Protein 3-D Structure Searching with Insertions and Deletions (2010)
  • Author(s): Tetsuo Shibuya, Jesper Jansson, Kunihiko Sadakane
  • Journal Title: BMC Algorithms for Molecular Biology 5
  • Peer Reviewed
• [Presentation] Statistical Model-based Algorithm Design Framework for Faster Protein Structure Database Searching (2010)
  • Author(s): Tetsuo Shibuya
  • Organizer: The 2010 Annual Conference of the Japanese Society for Bioinformatics
  • Place of Presentation: 九州大学 福岡県福岡市
  • Year and Date: 2010-12-15
• [Presentation] Linear-Time Protein 3-D Structure Searching with Insertions and Deletions (2009)
  • Author(s): Tetsuo Shibuya, Jesper Jansson, Kunihiko Sadakane
  • Organizer: 9th Workshop on Algorithms in Bioinformatics
  • Place of Presentation: 米国ペンシルベニア州フィラデルフィア
  • Year and Date: 2009-09-12
• [Presentation] Searching Protein 3-D Structures in Linear Time (2009)
  • Author(s): Tetsuo Shibuya
  • Organizer: 13th Annual International Conference on Research in Computational Molecular Biology
  • Place of Presentation: 米国アリゾナ州ツーソン
  • Year and Date: 2009-05-23
• [Presentation] 線形時間タンパク質3次元構造探索アルゴリズム (2009)
  • Author(s): 渋谷哲朗
  • Organizer: 情報処理学会アルゴリズム研究会
  • Place of Presentation: 小樽商科大学
  • Year and Date: 2009-03-05
• [Presentation] 線形時間タンパク質3次元構造探索アルゴリズム (2009)
  • Author(s): 渋谷哲朗
  • Organizer: 情報処理学会 アルゴリズム研究会 pp.25-32
  • Place of Presentation: IPSJ SIG Notes SIGAL 123-4
• [Presentation] Searching Protein 3-D Structures in Linear Time (2009)
  • Author(s): Tetsuo Shibuya
  • Organizer: Proc. 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2009) pp.1-15最優秀論文賞
  • Place of Presentation: LNCS 5817 (LNBI 5541)
• [Presentation] Linear-Time Protein 3-D Structure Searching with Insertions and Deletions (2009)
  • Author(s): Tetsuo Shibuya, Jesper Jansson, Kunihiko Sadakane
  • Organizer: 9th Workshop on Algorithms in Bioinformatics (WABI 2009) vol.5724, pp.310-320
  • Place of Presentation: LNCS
• [Remarks] 設計パラダイムSMADの紹介を以下のページで簡単に紹介している。
  • URL: http://shibuyalab.hgc.jp/SMAD.html
• [Remarks] SMAD技術紹介ページ
  • URL: http://shibuyalab.hgc.jp/SMAD.html
• [Remarks] Web page for the technique called SMAD
  • URL: http://shibuyalab.hgc.jp/SMAD.html