2014 Fiscal Year Annual Research Report
タンパク質・糖鎖相互作用予測システムおよびデータベースの開発
| Project/Area Number |
23300109
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| Research Institution | The University of Tokyo |
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Principal Investigator |
清水 謙多郎 東京大学, 農学生命科学研究科, 教授 (80178970)
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| Co-Investigator(Kenkyū-buntansha) |
寺田 透 東京大学, 農学生命科学研究科, 准教授 (40359641)
角越 和也 東京大学, 農学生命科学研究科, 助教 (90431832)
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| Project Period (FY) |
2011-04-01 – 2015-03-31
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| Keywords | タンパク質 / 糖 / 相互作用 / バイオインフォマティクス / データベース |
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| Outline of Annual Research Achievements |
We developed a prediction system that predicts sugar binding proteins and the sugar binding sites of the proteins from amino acid sequences using support vector machine (SVM). SVM is one of the representative techniques to classify data into two categories. SVM is known to have high generalization ability. A total of 366 sugar binding proteins were obtained from Protein Data Bank (PDB) for training the predictor under the following conditions: A sugar binding residue is defined as a residue that has an atom within 4 angstrom; from any atom of sugar, and a sugar binding protein is defined as a protein that has one or more sugar binding residues. The feature vector of sugar binding proteins and residues is created by using position-specific scoring matrix (PSSM). PSSM is created by PSI-BLAST for each sugar binding protein. We evaluated the prediction performance of this system by 5-fold cross validation. We built a workflow combining two prediction systems: the sugar binding protein prediction and the sugar binding site prediction, and launch this system on the web. An end user can use these predictors on the pipeline Galaxy with high flexibility. We exhibit this system as an open source and free ware in portal site UTProt (http://utprot.net/).
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| Research Progress Status |
26年度が最終年度であるため、記入しない。
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| Strategy for Future Research Activity |
26年度が最終年度であるため、記入しない。
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[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
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Journal Title
G3: Genes, Genomes, Genetics
Volume: Volume 5
Pages: 271～279
DOI
Peer Reviewed / Open Access
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[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
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Journal Title
Applied and Environmental Microbiology
Volume: Volume 80
Pages: 2821～2832
DOI
Peer Reviewed / Open Access
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