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Computational prediction of mitochondrial protein interactome

Research Project

Project/Area Number 18K18149
Research Category

Grant-in-Aid for Early-Career Scientists

Allocation TypeMulti-year Fund
Review Section Basic Section 62010:Life, health and medical informatics-related
Research InstitutionTokyo Institute of Technology

Principal Investigator

Ohue Masahito  東京工業大学, 情報理工学院, 助教 (50743209)

Project Period (FY) 2018-04-01 – 2021-03-31
Project Status Discontinued (Fiscal Year 2020)
Budget Amount *help
¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2020: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2019: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2018: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Keywordsバイオインフォマティクス / タンパク質間相互作用 / インタラクトーム / ミトコンドリアタンパク質
Outline of Final Research Achievements

A comprehensive understanding of mitochondrial proteins has been a major challenge in biology and medicine. In particular, protein-protein interactions (PPIs) involving mitochondrial proteins have been little investigated and information on them is scattered, although they are highly valuable as drug targets. The aim of this project was to develop a technology to elucidate the comprehensive interactome of mitochondrial proteins. We have developed an advanced PPI prediction technology, MEGADOCK. In addition, we developed a database of the results of the comprehensive PPI prediction, integrated the related information, and published it.

Academic Significance and Societal Importance of the Research Achievements

ミトコンドリアに存在するタンパク質はミトコンドリア病をはじめとする様々な疾病と関係しているため、治療手段の無い疾病のための薬の開発などにミトコンドリアタンパク質の理解を進めることが重要である。本研究では、タンパク質同士の相互作用という機能に着目し、そのような相互作用が行われているかを計算によって網羅的に予測することを行った。開発したデータベースであるMEGADOCK-Web-Mitoは自由にアクセスすることができ、創薬研究開発などの加速に貢献することが期待される。

Report

(3 results)
  • 2020 Final Research Report ( PDF )
  • 2019 Annual Research Report
  • 2018 Research-status Report
  • Research Products

    (45 results)

All 2020 2019 2018 Other

All Int'l Joint Research (2 results) Journal Article (12 results) (of which Int'l Joint Research: 1 results,  Open Access: 12 results,  Peer Reviewed: 10 results) Presentation (29 results) (of which Int'l Joint Research: 7 results,  Invited: 4 results) Remarks (2 results)

  • [Int'l Joint Research] CNRS/リヨン大学(フランス)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] CNRS/Lyon 1 University(フランス)

    • Related Report
      2018 Research-status Report
  • [Journal Article] Rescoring ensembles of protein-protein docking poses using consensus approaches2020

    • Author(s)
      Launay Guillaume、Ohue Masahito、Santero Julia Prieto、Matsuzaki Yuri、Hilpert C?cile、Uchikoga Nobuyuki、Hayashi Takanori、Martin Juliette
    • Journal Title

      bioRxiv

      Volume: 2020.04.24.059469

    • DOI

      10.1101/2020.04.24.059469

    • Related Report
      2019 Annual Research Report
    • Open Access / Int'l Joint Research
  • [Journal Article] Multidomain protein structure prediction using information about residues interacting on multimeric protein interfaces2020

    • Author(s)
      Matsuno Shumpei, Ohue Masahito, Akiyama Yutaka
    • Journal Title

      Biophysics and Physicobiology

      Volume: 17 Issue: 0 Pages: 2-13

    • DOI

      10.2142/biophysico.BSJ-2019050

    • NAID

      130007795865

    • ISSN
      2189-4779
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Multiple HPC Environments-Aware Container Image Configuration Workflow for Large-Scale All-to-All Protein?Protein Docking Calculations2020

    • Author(s)
      Aoyama Kento、Watanabe Hiroki、Ohue Masahito、Akiyama Yutaka
    • Journal Title

      In Proceedings of the 6th Asian Conference on Supercomputing Frontiers (SCFA2020), Lecture Notes in Computer Science

      Volume: 12082 Pages: 23-39

    • DOI

      10.1007/978-3-030-48842-0_2

    • ISBN
      9783030488413, 9783030488420
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Learning-to-rank technique based on ignoring meaningless ranking orders between compounds2019

    • Author(s)
      Ohue Masahito, Suzuki Shogo D., Akiyama Yutaka
    • Journal Title

      Journal of Molecular Graphics and Modelling

      Volume: 92 Pages: 192-200

    • DOI

      10.1016/j.jmgm.2019.07.009

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A playful tool for predicting protein-protein docking2019

    • Author(s)
      Jiang Keren、Zhang Di、Iino Tsubasa、Kimura Risa、Nakajima Tatsuo、Shimizu Kana、Ohue Masahito、Akiyama Yutaka
    • Journal Title

      In Proceedings of the 18th International Conference on Mobile and Ubiquitous Multimedia (MUM 2019)

      Volume: - Pages: 5-5

    • DOI

      10.1145/3365610.3368409

    • Related Report
      2019 Annual Research Report
    • Open Access
  • [Journal Article] Performance evaluation of MEGADOCK protein-protein interaction prediction system implemented with distributed containers on a cloud computing environment2019

    • Author(s)
      Kento Aoyama, Yuki Yamamoto, Masahito Ohue, Yutaka Akiyama
    • Journal Title

      In Proceedings of the 2019 International Conference on Parallel and Distributed Processing Techniques & Applications (PDPTA'19)

      Volume: - Pages: 175-181

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Molecular activity prediction using graph convolutional deep neural network considering distance on a molecular graph2019

    • Author(s)
      Masahito Ohue, Ryota Ii, Keisuke Yanagisawa, Yutaka Akiyama
    • Journal Title

      In Proceedings of the 2019 International Conference on Parallel and Distributed Processing Techniques & Applications (PDPTA'19)

      Volume: - Pages: 122-128

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Parallelized Pipeline for Whole Genome Shotgun Metagenomics with GHOSTZ-GPU and MEGAN2019

    • Author(s)
      Ohue Masahito、Yamasawa Marina、Izawa Kazuki、Akiyama Yutaka
    • Journal Title

      In Proceedings of the 19th annual IEEE International Conference on Bioinformatics and Bioengineering (IEEE BIBE 2019)

      Volume: - Pages: 152-156

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] NRLMFβ: Beta-distribution-rescored neighborhood regularized logistic matrix factorization for improving the performance of drug?target interaction prediction2019

    • Author(s)
      Ban Tomohiro、Ohue Masahito、Akiyama Yutaka
    • Journal Title

      Biochemistry and Biophysics Reports

      Volume: 18 Pages: 100615-100615

    • DOI

      10.1016/j.bbrep.2019.01.008

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques2018

    • Author(s)
      Tajimi Takashi、Wakui Naoki、Yanagisawa Keisuke、Yoshikawa Yasushi、Ohue Masahito、Akiyama Yutaka
    • Journal Title

      BMC Bioinformatics

      Volume: 19 Issue: S19 Pages: 527-527

    • DOI

      10.1186/s12859-018-2529-z

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] The DEAD-box RNA-binding protein DDX6 regulates parental RNA decay for cellular reprogramming to pluripotency.2018

    • Author(s)
      Kami D, Kitani T, Nakamura A, Wakui N, Mizutani R, Ohue M, Kametani F, Akimitsu N, Gojo S.
    • Journal Title

      PLoS One

      Volume: 13 Issue: 10 Pages: e0203708-e0203708

    • DOI

      10.1371/journal.pone.0203708

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions.2018

    • Author(s)
      Takanori Hayashi, Yuri Matsuzaki, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama
    • Journal Title

      BMC Bioinformatics

      Volume: 19 Issue: S4 Pages: 62-72

    • DOI

      10.1186/s12859-018-2073-x

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] Supercomputing-based exhaustive protein-protein interaction prediction with MEGADOCK2020

    • Author(s)
      Masahito Ohue
    • Organizer
      The 5th IITM-Tokyo Tech Joint Symposium-Current trends in bioinformatics: Big data analysis, machine learning and drug design
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] PKRank & SPDRank - Learning-to-rank methods for machine-learning-based drug discovery2020

    • Author(s)
      Masahito Ohue, Shogo D. Suzuki, Yutaka Akiyama
    • Organizer
      Biophysical Society 64th Annual Meeting
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Exhaustive protein-protein interaction prediction using MEGADOCK on a large-scale HPC environment2020

    • Author(s)
      Hiroki Watanabe, Masahito Ohue, Yutaka Akiyama
    • Organizer
      2nd RWBC-OIL Workshop
    • Related Report
      2019 Annual Research Report
  • [Presentation] Multiple HPC Environments-Aware Container Image Configuration Workflow for Large-Scale All-to-All Protein-Protein Docking Calculations2020

    • Author(s)
      Kento Aoyama, Hiroki Watanabe, Masahito Ohue, Yutaka Akiyama
    • Organizer
      2nd RWBC-OIL Workshop
    • Related Report
      2019 Annual Research Report
  • [Presentation] Improved protein-protein docking using arbitrary docking-derived protein interface predictions2020

    • Author(s)
      Max Druyvesteyn, Masahito Ohue, Yutaka Akiyama
    • Organizer
      2nd RWBC-OIL Workshop
    • Related Report
      2019 Annual Research Report
  • [Presentation] Multidomain protein structure prediction using information about residues interacting on multimeric protein interfaces2020

    • Author(s)
      Shunpei Matsuno, Masahito Ohue, Yutaka Akiyama
    • Organizer
      2nd RWBC-OIL Workshop
    • Related Report
      2019 Annual Research Report
  • [Presentation] マルチノード・マルチGPU上での網羅的なタンパク質間相互作用予測の高速化2020

    • Author(s)
      渡辺紘生, 大上雅史, 秋山泰
    • Organizer
      情報処理学会研究報告 バイオ情報学研究会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 薬のタネ探しを支援する計算技術2020

    • Author(s)
      大上雅史
    • Organizer
      LiHub創薬技術革新グループ ワークショップ 異分野融合による創薬研究
    • Related Report
      2019 Annual Research Report
  • [Presentation] Learning-to-rank for ligand-based virtual screening2019

    • Author(s)
      Masahito Ohue
    • Organizer
      AHeDD2019/IPAB2019 Joint Symposium
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Multiple HPC Environments-Aware Container Image Configuration for Bioinformatics Application2019

    • Author(s)
      Kento Aoyama, Hiroki Watanabe, Masahito Ohue, Yutaka Akiyama
    • Organizer
      International Conference for High Performance Computing, Networking, Storage, and Analysis (SC'19)
    • Related Report
      2019 Annual Research Report
  • [Presentation] Performance evaluation of MEGADOCK protein-protein interaction prediction system implemented with distributed containers on a cloud computing environment2019

    • Author(s)
      Kento Aoyama, Yuki Yamamoto, Masahito Ohue, Yutaka Akiyama
    • Organizer
      IPSJ Technical Report SIGMPS
    • Related Report
      2019 Annual Research Report
  • [Presentation] マルチドメインタンパク質の相互作用残基ペア予測を用いた立体構造予測手法の改良2019

    • Author(s)
      松野駿平, 大上雅史, 秋山泰
    • Organizer
      情報処理学会研究報告 バイオ情報学研究会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 薬のタネを探すインフォマティクス技術2019

    • Author(s)
      大上雅史
    • Organizer
      第42回日本分子生物学会年会, [1F-06]フォーラム 薬効評価・予測技術の進歩による創薬研究の加速
    • Related Report
      2019 Annual Research Report
  • [Presentation] PKRank & SPDRank 化合物選別のためのランク学習法2019

    • Author(s)
      大上雅史, 鈴木翔吾, 秋山泰
    • Organizer
      生命情報科学若手の会第11回研究会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Acceleration and virtualization of parallel protein-protein interaction prediction system MEGADOCK2019

    • Author(s)
      Masahito Ohue, Hiroki Watanabe, Kento Aoyama, Yutaka Akiyama
    • Organizer
      The 57th Annual Meeting of the Biophysical Society of Japan
    • Related Report
      2019 Annual Research Report
  • [Presentation] PKRank & SPDRank: Learning-to-rank methods for ligand-based virtual screening2019

    • Author(s)
      Masahito Ohue, Shogo D. Suzuki, Yutaka Akiyama
    • Organizer
      第8回生命医薬情報学連合大会 (IIBMP2019)
    • Related Report
      2019 Annual Research Report
  • [Presentation] Multiple HPC Environments-Aware Container Image Configuration for Bioinformatics Application2019

    • Author(s)
      Kento Aoyama, Hiroki Watanabe, Masahito Ohue, Yutaka Akiyama
    • Organizer
      第8回生命医薬情報学連合大会 (IIBMP2019)
    • Related Report
      2019 Annual Research Report
  • [Presentation] Accelerating MEGADOCK: protein-protein interaction prediction software on multiple nodes and multiple GPUs environment2019

    • Author(s)
      Hiroki Watanabe, Masahito Ohue, Yutaka Akiyama
    • Organizer
      第8回生命医薬情報学連合大会 (IIBMP2019)
    • Related Report
      2019 Annual Research Report
  • [Presentation] Multidomain protein structure prediction using multimeric interaction residue pair information2019

    • Author(s)
      Shumpei Matsuno, Masahito Ohue, Yutaka Akiyama
    • Organizer
      第8回生命医薬情報学連合大会 (IIBMP2019)
    • Related Report
      2019 Annual Research Report
  • [Presentation] バイオデ―タと戦う情報学2019

    • Author(s)
      大上雅史
    • Organizer
      情報学の次世代検討会Ⅰ
    • Related Report
      2019 Annual Research Report
  • [Presentation] MEGADOCK-Web: An Integrated Database of High-Throughput Structure-Based Protein-Protein Interaction Predictions2019

    • Author(s)
      Masahito Ohue, Takanori Hayashi, Yuri Matsuzaki, Keisuke Yanagisawa, Yutaka Akiyama
    • Organizer
      Biophysical Society 63rd Annual Meeting
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] High Performance Computing Drug Discovery - Toward Targeting Protein-Protein Interactions2018

    • Author(s)
      Masahito Ohue
    • Organizer
      Advances in Neuroinformatics 2018 (AINI2018)
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Prediction of Protein-Protein Interactions with MEGADOCK: Parallelization, Application, and Open Database2018

    • Author(s)
      Masahito Ohue
    • Organizer
      Asia Hub e-Drug Discovery Symposium (AHeDD2018)
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Supercomputing-based exhaustive protein-protein interaction prediction and its open database2018

    • Author(s)
      Masahito Ohue
    • Organizer
      The 56th Annual Meeting of the Biophysical Society of Japan
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] MEGADOCK: a supercomputing bioinformatics application for protein-protein interaction prediction2018

    • Author(s)
      Masahito Ohue
    • Organizer
      1st RWBC-OIL Workshop
    • Related Report
      2018 Research-status Report
  • [Presentation] MEGADOCK-Web-Mito: a database of computer-predicted mitochondrial protein-protein interactions2018

    • Author(s)
      Hiroki Watanabe, Takanori Hayashi, Masahito Ohue, Yutaka Akiyama
    • Organizer
      1st RWBC-OIL Workshop
    • Related Report
      2018 Research-status Report
  • [Presentation] ミトコンドリアに関連したヒトタンパク質間相互作用予測データベースMEGADOCK-Web-Mitoの開発2018

    • Author(s)
      渡辺紘生, 林孝紀, 大上雅史, 秋山泰
    • Organizer
      情報処理学会研究報告 バイオ情報学
    • Related Report
      2018 Research-status Report
  • [Presentation] 新しい創薬標的の探索を支えるインフォマティクス技術2018

    • Author(s)
      大上雅史
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Research-status Report
  • [Presentation] タンパク質複合体構造モデリングの評価のためのベンチマークデータセット2018

    • Author(s)
      林孝紀, 大上雅史, Juliette Martin, Guillaume Launay, 松崎由理, 内古閑伸之, 秋山泰
    • Organizer
      第56回日本生物物理学会年会
    • Related Report
      2018 Research-status Report
  • [Remarks]

    • URL

      https://www.bi.cs.titech.ac.jp/~ohue

    • Related Report
      2019 Annual Research Report
  • [Remarks]

    • URL

      http://www.bi.cs.titech.ac.jp/~ohue

    • Related Report
      2018 Research-status Report

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Published: 2018-04-23   Modified: 2022-01-27  

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