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Development of protein-carbohydrate binding prediction systems and databases

Research Project

Project/Area Number 23300109
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Bioinformatics/Life informatics
Research InstitutionThe University of Tokyo

Principal Investigator

SHIMIZU Kentaro  東京大学, 農学生命科学研究科, 教授 (80178970)

Co-Investigator(Kenkyū-buntansha) TERADA Tohru  東京大学, 大学院農学生命科学研究科, 准教授 (40359641)
SUMIKOSHI Kazuya  東京大学, 大学院農学生命科学研究科, 助教 (90431832)
Project Period (FY) 2011-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥18,980,000 (Direct Cost: ¥14,600,000、Indirect Cost: ¥4,380,000)
Fiscal Year 2014: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2013: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2012: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000)
Fiscal Year 2011: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Keywordsタンパク質 / 糖鎖 / 相互作用予測 / データベース / バイオインフォマティクス / 糖 / 相互作用 / 予測機能
Outline of Final Research Achievements

In this study, we developed the prediction methods of carbohydrate binding proteins (predicting whether a given protein binds to the carbohydrate), protein-carbohydrate binding sites (predicting which residues bind to the carbohydrate), binding carbohydrates (predicting what kinds of carbohydrate bind to a given protein), complex structures of protein and carbohydrate, glycosylation sites. We also developed the comprehensive databases of protein-carbohydrates which contain sequences, structures, binding ligands, and a variety of information about the function.

Report

(5 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • Research Products

    (46 results)

All 2015 2014 2013 2012 2011 Other

All Journal Article (18 results) (of which Peer Reviewed: 18 results,  Open Access: 8 results,  Acknowledgement Compliant: 2 results) Presentation (25 results) (of which Invited: 2 results) Remarks (3 results)

  • [Journal Article] Overdominance effect of the bovine ghrelin receptor (GHSR1a)-DelR242 locus on growth in Japanese Shorthorn weaner bulls: Heterozygote advantage in bull selection and molecular mechanisms.2015

    • Author(s)
      Masanori Komatsu, Yoichi Sato, Tatsuki Negami, Tohru Terada, Osamu Sasaki, Jumpei Yasuda, Aisaku Arakawa, Chikara Yoshida, Hideaki Takahashi, Aduli E.O. Malau-Aduli, Keiichi Suzuki and Kentaro Shimizu
    • Journal Title

      G3: Genes, Genomes, Genetics

      Volume: Volume 5 Issue: 2 Pages: 271-279

    • DOI

      10.1534/g3.114.016105

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Coarse-Grained Molecular Dynamics Simulations of Protein-Ligand Binding2014

    • Author(s)
      Tatsuki Negami, Kentaro Shimizu, Tohru Terada
    • Journal Title

      Journal of Computational Chemistry

      Volume: Volume 35 Issue: 25 Pages: 1835-1845

    • DOI

      10.1002/jcc.23693

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structural Basis of the Divergent Oxygenation Reactions Catalyzed by the Rieske Nonheme Iron Oxygenase Carbazole 1,9a-Dioxygenase2014

    • Author(s)
      Kengo Inoue, Yusuke Usami, Yuji Ashikawa, Haruko Noguchi, Takashi Umeda, Aiko Yamagami-Ashikawa, Tadafumi Horisaki, Hiromasa Uchimura, Tohru Terada, Shugo Nakamura, Kentaro Shimizu, Hiroshi Habe, Hisakazu Yamane, Zui Fujimoto and Hideaki Nojiri
    • Journal Title

      Applied and Environmental Microbiology

      Volume: Volume 80 Issue: 9 Pages: 2821-2832

    • DOI

      10.1128/aem.04000-13

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Linked Open Data Construction of Purpose Oriented Interactomics by Integration of Life Sciences LOD2014

    • Author(s)
      込山 悠介, 番野 雅城, 鑓水 優行, 加藤 文彦, 大向 一輝, 武田 英明, 清水 謙多郎
    • Journal Title

      Transactions of the Japanese Society for Artificial Intelligence

      Volume: 29 Issue: 4 Pages: 356-363

    • DOI

      10.1527/tjsai.29.356

    • NAID

      130004927341

    • ISSN
      1346-0714, 1346-8030
    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Engineering the allosteric properties of archaeal non-phosphorylating glyceraldehyde-3-phosphate dehydrogenases.2014

    • Author(s)
      Fumiaki Ito, Masayuki Miyake, Shinya Fushinobu, Shugo Nakamura, Kentaro Shimizu, Takayoshi Wakagi
    • Journal Title

      BBA - Proteins and Proteomics

      Volume: Volume 1844 Issue: 4 Pages: 759-766

    • DOI

      10.1016/j.bbapap.2014.01.017

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] TCC: an R package for comparing tag count data with robust normalization strategies.2013

    • Author(s)
      Sun, J., Nishiyama, T., Shimizu, K., and Kadota, K.
    • Journal Title

      BMC Bioinformatics

      Volume: 14 Issue: 1 Pages: 219-219

    • DOI

      10.1186/1471-2105-14-219

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Selective binding of antimicrobial porphyrins to the hame-receptor IsdH-NEAT3 of Staphylococcus aureus.2013

    • Author(s)
      Nhuan Vu
    • Journal Title

      Protein Science

      Volume: 22 Issue: 7 Pages: 942-953

    • DOI

      10.1002/pro.2276

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Heme binding mechanism of structurally similar iron-regulated surface determinant near transporter domains of Staphylococcus aureus exhibiting different affinities for heme.2013

    • Author(s)
      Yoshitaka Moriwaki
    • Journal Title

      Biochemistry

      Volume: 52 Issue: 49 Pages: 8866-8877

    • DOI

      10.1021/bi4008325

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A new method for evaluating the specificity of indirect readout in protein-DNA recognition2012

    • Author(s)
      S. Yamasaki
    • Journal Title

      Nucleic Acids Res

      Volume: Vol. 40 Issue: 20 Pages: e135-e135

    • DOI

      10.1093/nar/gkp718

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A new entropy model for RNA: part III, Is the folding free energy landscape of RNA funnel shaped?2012

    • Author(s)
      W. Dawson
    • Journal Title

      Journal of Nucleic Acids Investigation

      Volume: Vol. 3, No. 1

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A new entropy model for RNA: part II, Persistence-related entropic contributions to RNA secondary structure free energy calculation.2012

    • Author(s)
      W. Dawson
    • Journal Title

      Journal of Nucleic Acids Investigation

      Volume: Vol. 3, No. 1

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A normalization strategy for comparing tag count data2012

    • Author(s)
      Kadota K., Nishiyama T., Shimizu K.
    • Journal Title

      Algorithms Mol. Biol.

      Volume: 7 Issue: 1 Pages: 5-5

    • DOI

      10.1186/1748-7188-7-5

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Small-angle X-ray scattering constraints and local geometry like secondary structures can construtct a coarse-grained protein model at amino acid residue resolution.2012

    • Author(s)
      Y. Morimoto
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: Volume 431 Issue: 1 Pages: 6569-6569

    • DOI

      10.1016/j.bbrc.2012.12.091

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A new entropy model for RNA : partIII, Is the folding free energy landscape of RNA funnel shaped?2012

    • Author(s)
      W.Dawson
    • Journal Title

      Journal of Nucleic Acids Investigation

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A new entropy model for RNA : partII, Persistence-related entropic contributions to RNA secondary structure free energy calculation2012

    • Author(s)
      W.Dawson
    • Journal Title

      Journal of Nucleic Acids Investigation

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] BUDDY-system : A web site for constructing a dataset of protein pairs between ligand-bound and unbound states2011

    • Author(s)
      M. Morita, T. Terada, S. Nakamura, K. Shimizu
    • Journal Title

      BMC Res. Notes

      Volume: 4 Issue: 1 Pages: 143-143

    • DOI

      10.1186/1756-0500-4-143

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Prediction of N-myristoylation modification of proteins by SVM2011

    • Author(s)
      W.Cao
    • Journal Title

      Bioinformation

      Pages: 204-206

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Protein-protein docking using multi-layered spherical basis functions2011

    • Author(s)
      K.Sumikoshi
    • Journal Title

      Proceeding of the 2011 Internatinaol Conference on Bioscience, Biochemistry and Bioinformatics

      Pages: 342-347

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Presentation] The factors determining protein-ligand binding processes revealed by comparative coarse-grained simulations2014

    • Author(s)
      Tatsuki Negami, Tohru Terada, Kentaro Shimizu
    • Organizer
      第52回日本生物物理学会年会
    • Place of Presentation
      札幌コンベンションセンター(北海道、札幌市)
    • Year and Date
      2014-09-26
    • Related Report
      2014 Annual Research Report
  • [Presentation] Structural insight into the heme-transfer mechanism between Isd proteins in Staphylococcus aureus2014

    • Author(s)
      Yoshitaka Moriwaki, Tohru Terada, Jose M. M. Caaveiro, Kouhei Tsumoto, Kentaro Shimizu
    • Organizer
      第52回日本生物物理学会年会
    • Place of Presentation
      札幌コンベンションセンター(北海道、札幌市)
    • Year and Date
      2014-09-26
    • Related Report
      2014 Annual Research Report
  • [Presentation] Effect of basis selection in reconstructing NMR spectra using compressed sensing2014

    • Author(s)
      Kazuya Sumikoshi, Teppei Ikeya, Yutaka Ito, Kentaro Shimizu
    • Organizer
      第52回日本生物物理学会年会
    • Place of Presentation
      札幌コンベンションセンター(北海道、札幌市)
    • Year and Date
      2014-09-25
    • Related Report
      2014 Annual Research Report
  • [Presentation] 位置特異的スコアリングマトリックスとサポートベクターマシーンを用いた脂質結合タンパク予測手法の開発2014

    • Author(s)
      植木快、番野雅城、中村周吾、清水謙多郞
    • Organizer
      第14回日本蛋白質科学会年会
    • Place of Presentation
      横浜産貿ホールマリネリア(神奈川県、横浜市)
    • Year and Date
      2014-06-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] タンパク質の複合体構造・相互作用に関する総合的な予測・解析/Prediction and analysis of protein complex structures and protein interactions2014

    • Author(s)
      清水謙多郞、寺田透
    • Organizer
      第14回日本蛋白質科学会年会
    • Place of Presentation
      ワークピア横浜(神奈川県、横浜市)
    • Year and Date
      2014-06-25
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] HEME-TRANSFER MECHANISM OF STRUCTURALLY SIMILAR ISD NEAT DOMAINS OF STAPHYLOCOCCUS AUREUS EXHIBITING DIFFERENT AFFINITIES FOR HEME.2014

    • Author(s)
      Yoshitaka Moriwaki, Tohru Terada, Jose M. M. Caaveiro, Yousuke Takaoka, Itaru Hamachi, Kouhei Tsumoto, Kentaro Shimizu
    • Organizer
      Biophysical Society, 58th Annual Meeting
    • Place of Presentation
      サンフランシスコ(アメリカ)
    • Year and Date
      2014-02-19
    • Related Report
      2013 Annual Research Report
  • [Presentation] PROTEIN-LIGAND BINDING SIMULATIONWITHTHE MARTINI COARSE-GRAINED FORCE FIELD.2014

    • Author(s)
      Tatsuki Negami, Tohru Terada, Kentaro Shimizu
    • Organizer
      Biophysical Society, 58th Annual Meeting
    • Place of Presentation
      サンフランシスコ(アメリカ)
    • Year and Date
      2014-02-18
    • Related Report
      2013 Annual Research Report
  • [Presentation] 蛋白質立体構造および相互作用の予測2013

    • Author(s)
      清水 謙多郎
    • Organizer
      第4回神経科学と構造生物学の融合研究会
    • Place of Presentation
      岡崎コンファレンスセンター(愛知県岡崎市)
    • Year and Date
      2013-11-19
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 代謝型グルタミン酸受容体の活性化過程の動的モデルの構築2013

    • Author(s)
      冨士原 海太、根上 樹、寺田 透、清水 謙多郎
    • Organizer
      日本生物物理学会 第51回年会
    • Place of Presentation
      国立京都国際会館(京都府京都市)
    • Year and Date
      2013-10-30
    • Related Report
      2013 Annual Research Report
  • [Presentation] 黄色ブドウ球菌のIsd-NEATドメイン間におけるヘム輸送についての考察2013

    • Author(s)
      Yoshitaka Moriwaki, Tohru Terada, Jose M. M. Caaveiro, Yousuke Takaoka, Itaru Hamachi, Kouhei Tsumoto, Kentaro Shimizu
    • Organizer
      日本生物物理学会 第51回年会
    • Place of Presentation
      国立京都国際会館(京都府京都市)
    • Year and Date
      2013-10-30
    • Related Report
      2013 Annual Research Report
  • [Presentation] Sequence derived predictor of lipid-binding proteins with support vector machine2013

    • Author(s)
      植木 快、込山 悠介、番野 雅城、中村 周吾、清水 謙多郎
    • Organizer
      日本バイオインフォマティクス学会 2013年年会
    • Place of Presentation
      タワーホール船堀(東京都江戸川区)
    • Year and Date
      2013-10-29
    • Related Report
      2013 Annual Research Report
  • [Presentation] UTProt: Database Integration and Tool Development for Interactomics Utilizing Biosemantics2013

    • Author(s)
      込山 悠介、番野 雅城、Gul Saad、遣水 優行、植木 快、清水 謙多郎
    • Organizer
      日本バイオインフォマティクス学会 2013年年会
    • Place of Presentation
      タワーホール船堀(東京都江戸川区)
    • Year and Date
      2013-10-29
    • Related Report
      2013 Annual Research Report
  • [Presentation] Development of system that predict sugar binding protein and sugar binding site based on protein sequence using support vector machine.2013

    • Author(s)
      番野 雅城、込山 悠介、中村 周吾、清水 謙多郎
    • Organizer
      日本バイオインフォマティクス学会 2013年年会
    • Place of Presentation
      タワーホール船堀(東京都江戸川区)
    • Year and Date
      2013-10-29
    • Related Report
      2013 Annual Research Report
  • [Presentation] 圧縮センシングを用いたNMRスペクトルの復元法2013

    • Author(s)
      Kazuya Sumikoshi, Teppei Ikeya, Yutaka Ito, Kentaro Shimizu
    • Organizer
      日本生物物理学会 第51回年会
    • Place of Presentation
      国立京都国際会館(京都府京都市)
    • Year and Date
      2013-10-29
    • Related Report
      2013 Annual Research Report
  • [Presentation] MARTINI粗視化力場を用いたタンパク質-リガンド結合過程の比較シュミレーション2013

    • Author(s)
      根上 樹、寺田 透、清水 謙多郎
    • Organizer
      日本生物物理学会 第51回年会
    • Place of Presentation
      国立京都国際会館(京都府京都市)
    • Year and Date
      2013-10-29
    • Related Report
      2013 Annual Research Report
  • [Presentation] 黄色ブドウ球菌のヘム輸送蛋白質群Isd system におけるその構造類似性とヘムの不可逆輸送に関する考察2013

    • Author(s)
      Yoshitaka Moriwaki, Tohru Terada, Jose M. M. Caaveiro, Yousuke Takaoka, Itaru Hamachi, Kouhei Tsumoto, Kentaro Shimizu
    • Organizer
      第13回日本蛋白質科学会年会
    • Place of Presentation
      とりぎん文化会館(鳥取県鳥取市)
    • Year and Date
      2013-06-12
    • Related Report
      2013 Annual Research Report
  • [Presentation] サポートベクターマシンを用いた糖鎖結合部位予測手法の開発2012

    • Author(s)
      番野 雅城
    • Organizer
      日本生物物理学会 第50回年会
    • Place of Presentation
      名古屋大学
    • Related Report
      2012 Annual Research Report
  • [Presentation] Prediction of the types of carbohydrate-binding proteins2012

    • Author(s)
      葛 臻翼
    • Organizer
      日本生物物理学会 第50回年会
    • Place of Presentation
      名古屋大学
    • Related Report
      2012 Annual Research Report
  • [Presentation] アミノ酸保存度と相互作用エネルギーを組み合わせたタンパク質―リガンド結合部位予測手法の開発2012

    • Author(s)
      辻川 寛人
    • Organizer
      日本生物物理学会 第50回年会
    • Place of Presentation
      名古屋大学
    • Related Report
      2012 Annual Research Report
  • [Presentation] タンパク質へのリガンド結合過程の粗視化シュミレーション:タンパク質の立体構造変化の影響の解析2012

    • Author(s)
      根上 樹
    • Organizer
      日本生物物理学会 第50回年会
    • Place of Presentation
      名古屋大学
    • Related Report
      2012 Annual Research Report
  • [Presentation] 計算化学と実験から考察した黄色ブドウ球菌のヘム鉄結合・輸送機構解析2012

    • Author(s)
      森脇 由隆
    • Organizer
      日本生物物理学会 第50回年会
    • Place of Presentation
      名古屋大学
    • Related Report
      2012 Annual Research Report
  • [Presentation] Finding discriminative genes in drug-dose responses from gene expression profiles of the multiple sclerosis disease2011

    • Author(s)
      O.Hirose
    • Organizer
      Genome Informatics Workshop 2011
    • Place of Presentation
      Busan, KOREA
    • Year and Date
      2011-12-05
    • Related Report
      2011 Annual Research Report
  • [Presentation] Development of an energy-based method for protein ligand binding site prediction2011

    • Author(s)
      Y.Umeda
    • Organizer
      Genome Informatics Workshop 2011
    • Place of Presentation
      Busan, KOREA
    • Year and Date
      2011-12-05
    • Related Report
      2011 Annual Research Report
  • [Presentation] Protein-ligand binding simulation with a coarse-graind force field, MARTINI2011

    • Author(s)
      T.Negami
    • Organizer
      日本生物物理学会第49回年会
    • Place of Presentation
      姫路
    • Year and Date
      2011-09-18
    • Related Report
      2011 Annual Research Report
  • [Presentation] Development of a method for predicting carbohtdrate-binding proteins2011

    • Author(s)
      Z.Ge
    • Organizer
      日本生物物理学会第49回年会
    • Place of Presentation
      姫路
    • Year and Date
      2011-09-16
    • Related Report
      2011 Annual Research Report
  • [Remarks] lipid-binding protein predictor

    • URL

      http://ec2-54-64-162-67.ap-northeast-1.compute.amazonaws.com/LBPredictor/default/index

    • Related Report
      2014 Annual Research Report 2013 Annual Research Report
  • [Remarks] 東京大学大学院農学生命科学研究科応用生命工学専攻生物情報工学研究室ホームページ

    • URL

      http://www.bi.a.u-tokyo.ac.jp/papers/

    • Related Report
      2014 Annual Research Report 2013 Annual Research Report
  • [Remarks] レクチン予測システム

    • URL

      http://www.bi.a.u-tokyo.ac.jp/software.html

    • Related Report
      2012 Annual Research Report

URL: 

Published: 2011-04-06   Modified: 2019-07-29  

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