Development of protein interaction prediction methods by modeling protein substructures

• Project/Area Number: 24500361
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Bioinformatics/Life informatics
• Research Institution: Kyoto University
• Principal Investigator: Hayashida Morihiro 京都大学, 化学研究所, 助教 (40402929)
• Project Period (FY): 2012-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000); Fiscal Year 2015: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2014: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2013: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2012: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
• Keywords: 条件付き確率場 / タンパク質RNA複合体 / タンパク質複合体 / SIFT特徴量 / タンパク質相互作用強度 / オンライン学習 / 中央文字列 / 中心文字列 / 整数計画法 / タンパク質立体構造 / SIFT / SURF / カーネル関数 / サポートベクトルマシン / 正則化 / タンパク質RNA相互作用 / 生体生命情報学 / アルゴリズム / タンパク質 / 機械学習

Outline of Final Research Achievements

We developed a similarity measure between protein tertiary structures using SIFT local feature descriptor, which is often used in the field of image recognition. The proposed measure outperforms previously developed measures based on image compression. Furthermore, we proposed conditional random field models for predicting residue-base contacts in protein-RNA complexes. In addition, we developed methods for predicting protein heterodimers and heterotrimers in higher accuracy than existing methods.

Research Products

• [Journal Article] Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order (2016)
  • Author(s): J. Jindalertudomdee, M. Hayashida, Y. Zhao, T. Akutsu
  • Journal Title: BMC Bioinformatics Volume: 17 Issue: 1 Pages: 113-113
  • DOI: 10.1186/s12859-016-0962-4
  • NAID: 120005822781
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Grammar-based compression approach to extraction of common rules among multiple trees of glycans and RNAs (2015)
  • Author(s): Y. Zhao, M. Hayashida, Y. Cao, J. Hwang, T. Akutsu
  • Journal Title: BMC Bioinformatics Volume: 16 Issue: 1 Pages: 128-128
  • DOI: 10.1186/s12859-015-0558-4
  • NAID: 120005749951
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Parallelization of enumerating tree-like chemical compounds by breadth-first search order (2015)
  • Author(s): M. Hayashida, J. Jindalertudomdee, Y. Zhao, T. Akutsu
  • Journal Title: BMC Medical Genomics Volume: 8 (Suppl 2) Issue: S2
  • DOI: 10.1186/1755-8794-8-s2-s15
  • NAID: 120005947140
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Prediction of Protein-protein Interaction Strength Using Domain Features with Supervised Regression (2014)
  • Author(s): Kamada, M., Sakuma, Y., Hayashida, M., Akutsu, T.
  • Journal Title: The Scientific World Journal Volume: 2014 Pages: 240673-240673
  • DOI: 10.1155/2014/240673
  • NAID: 120005462601
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Proteome Compression via Protein Domain Compositions (2014)
  • Author(s): Hayashida, M., Ruan, P., Akutsu, T.
  • Journal Title: Methods Volume: 67 Issue: 3 Pages: 380-385
  • DOI: 10.1016/j.ymeth.2014.01.012
  • NAID: 120005466444
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Prediction of heterodimeric protein complexes from weighted protein-protein interaction networks using novel features and kernel functions (2013)
  • Author(s): Peiying Ruan, Morihiro Hayashida, Osamu Maruyama, Tatsuya Akutsu
  • Journal Title: PLoS ONE Volume: 8 Issue: 6 Pages: e65265-e65265
  • DOI: 10.1371/journal.pone.0065265
  • NAID: 120005296009
  • Peer Reviewed
• [Journal Article] Prediction of protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso (2013)
  • Author(s): Hayashida, M., Kamada, M., Song, J., Akutsu, T.
  • Journal Title: BMC Systems Biology Volume: 7 Issue: Suppl 2 Pages: S15-S15
  • DOI: 10.1186/1752-0509-7-s2-s15
  • Peer Reviewed
• [Journal Article] Prediction of heterotrimeric protein complexes by two-phase learning using neighboring kernels (2013)
  • Author(s): Ruan, P., Hayashida, M., Maruyama, O., Akutsu, T.
  • Journal Title: BMC Bioinformatics Volume: 15 Issue: S2
  • DOI: 10.1186/1471-2105-15-s2-s6
  • NAID: 120005372925
  • Peer Reviewed
• [Journal Article] Survival analysis by penalized regression and matrix factorization (2013)
  • Author(s): Yeuntyng Lai, Morihiro Hayashida, Tatsuya Akutsu
  • Journal Title: The Scientific World Journal Volume: 2013 Issue: 1 Pages: 632030-632030
  • DOI: 10.1155/2013/632030
  • NAID: 120005289846
  • Peer Reviewed
• [Presentation] Integer linear programming approach to median and center strings for a probability distribution on a set of strings (2016)
  • Author(s): Hayashida, M., Koyano, H.
  • Organizer: The 7th International Conference on Bioinformatics Models, Methods and Algorithms
  • Place of Presentation: Rome, Italy
  • Year and Date: 2016-02-21
  • Int'l Joint Research
• [Presentation] Online learning approach to prediction of protein-protein interaction strengths (2015)
  • Author(s): Hayashida, M., Kamada, M., Koyano, H.
  • Organizer: The 9th International Conference on Systems Biology
  • Place of Presentation: Luoyang, China
  • Year and Date: 2015-08-21
  • Int'l Joint Research
• [Presentation] Measuring the Similarity of Protein Structures Using Image Local Feature Descriptors SIFT and SURF (2014)
  • Author(s): Hayashida, M., Koyano, H., Akutsu, T.
  • Organizer: The 8th International Conference on Systems Biology
  • Place of Presentation: Qingdao, China
  • Year and Date: 2014-10-24 – 2014-10-27
• [Presentation] Parallelization of Enumerating Tree-like Chemical Compounds by Breadth-first Search Order (2014)
  • Author(s): Hayashida, M., Jindalertudomdee, J., Zhao, Y., Akutsu, T.
  • Organizer: The 8th International Conference on Systems Biology
  • Place of Presentation: Qingdao, China
  • Year and Date: 2014-10-24 – 2014-10-27
• [Presentation] Predicting protein-RNA residue-base contacts using two-dimensional conditional random field (2012)
  • Author(s): Morihiro Hayashida, Mayumi Kamada, Jiangning Song, Tatsuya Akutsu
  • Organizer: 2012 IEEE Conference on Systems Biology
  • Place of Presentation: Xi'an, China
• [Presentation] Inferring strengths of protein-protein interactions using support vector regression
  • Author(s): Sakuma, Y., Kamada, M., Hayashida, M., Akutsu, T.
  • Organizer: The 2013 International Conference on Parallel and Distributed Processing Techniques and Applications
  • Place of Presentation: Las Vegas, USA
• [Presentation] Proteome compression via protein domain compositions
  • Author(s): Hayashida, M., Ruan, P., Akutsu, T.
  • Organizer: 2013 IEEE Conference on Systems Biology
  • Place of Presentation: Huangshan, China
• [Presentation] Prediction of heterotrimeric protein complexes by two-phase learning using neighboring kernels
  • Author(s): Ruan, P., Hayashida, M., Maruyama, O., Akutsu, T.
  • Organizer: The 12th Asia Pacific Bioinformatics Conference
  • Place of Presentation: Shanghai, China
• [Presentation] Study on weight of protein-protein interaction network for prediction of heterodimers
  • Author(s): Ruan, P., Hayashida, M., Akutsu, T.
  • Organizer: 電子情報通信学会総合大会
  • Place of Presentation: 新潟大学