2002 Fiscal Year Final Research Report Summary
the maintenance and circulation of protein higher-order structural information and the evaluation of prediction information
| Project/Area Number |
12207002
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| Research Category |
Grant-in-Aid for Scientific Research on Priority Areas
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| Allocation Type | Single-year Grants |
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| Review Section |
Biological Sciences
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| Research Institution | Nagoya University |
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Principal Investigator |
GO Mitiko Nagoya University, Department of Biology Faculty of Science, Professor, 大学院理学研究科, 教授 (70037290)
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| Co-Investigator(Kenkyū-buntansha) |
NISHIKAWA Ken National Institute of Genetics, Centre for Information Biology and DNAData Bank of Japan, Professor, DDBJ研究センター, 教授 (10093288)
MITAKU Shigeki Tokyo University of Agriculture and Technology, Faculty of Engineering, Professor, 工学部, 教授 (10107542)
UMEYAMA Hideaki Kitasato University, School of Pharmaceutical Sciences, Professor, 薬学部, 教授 (20050619)
KIDERA Akinori Yokohama City University, Graduate School of Integrated Science, Professor, 大学院総合理学研究科, 教授 (00186280)
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| Project Period (FY) |
2000 – 2002
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| Keywords | Computational biology / Bioinformatics / Genome function prediction / Protein structure prediction / Critical Assessment of Techniques for Protein Structure Prediction / Homology modeling / FAMSBASE / Molecular simulation |
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| Research Abstract |
Mainly through the following research products and activities for three years, we conducted the maintenance and circulation of protein higher-order structural information and the evaluation of prediction information.
Every year we held the open workshop of "Genome Information Science Based on Protein Higher-order Structures (Higher-order Genome)", including poster presentations of the "Higher-order Genome" group and a one-day symposium. In the first year, we invited two overseas speakers from the field of protein architecture and bioinformatics and held an international symposium. In the second year, in preparation for coming days of higher-order structural information flood according to rapid progress of the structural genomics, we held the open symposium titled "Information Biology as Structural Genome Science--When All Protein Structures of the Representative Proteins Are Clarified--", enhancing cooperation with structural biologists. Decoding of genome information would be incomplet
… More
e without understanding of proteins, main actors playing direct roles for physiological phenomena, and simulation studies are occupying an important position as a means for that aim. In the third year, we thus held the international symposium titled "Frontier Bioinformatics--To What Extent Can Simulations Clarify Protein Functions?", where four overseas researchers were invited.
"One-day symposium of computational structural genomics" was also held as a satellite meeting of "International Conference on Structural Genomics (ICSG) in 2000. Additionally, we executed various activities including research meetings of the "Higher-order Genome" group, support of young researcher's study meetings, travel support to attend the international meeting of "Critical Assessment of Techniques for Protein Structure Prediction (CASP)" and cooperation with alga researchers in "Genome Biology".
On the other hand, we constructed as complete sets of comparative protein structure models as possible for the whole genome ORFs presented in GTOP database and publicly released as FAMSBASE (http://daisy.nagahama-i-bio.ac.jp/Famsbase/). A statistical analysis of the data was also published. Less
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[Journal Article] Evaluation of the third solvent clusters fitting procedure for the prediction of protein-protein interactions based on the results at the CAPRI blind docking study2003
Author(s)
Komatsu, K., Kurihara, Y., Iwadate, M., Takeda-Shitaka, M., Umeyama, H.
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Journal Title
PROTEINS, Structure, Function and Genetics 52(1)
Pages: 15-18
Description
「研究成果報告書概要(和文)」より
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[Journal Article] Enlarged FAMSBASE : 3D protein structure models of genome sequences for 41 species2003
Author(s)
Yamaguchi, A., Iwadate, M., Suzuki, E., Yura, K., Kawakita, S., Umeyama.H., Go, M.
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Journal Title
Nucleic Acids Research 31(1)
Pages: 463-468
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] GTOP : A database of protein structures predicted from genome sequences2002
Author(s)
Kawabata.T., Fukuchi, S., Homma, K., Ota, M., Araki, J., Ito, T., Ichiyoshi, N., Nishikawa.K.
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Journal Title
Nucl.Acids Res. 30(1)
Pages: 294-298
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] KdsA mutations affect FtsZ-ring formation in Escherichia coli K-122002
Author(s)
Fujishima, H., Nishimura, A., Wachi, M., Takagi, H., Hirasawa, T.Teraoka, H., Nishimori, K., Kawabata, T., Nishikawa, K., Nagai, K.
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Journal Title
Microbiology 148(pt1)
Pages: 103-112
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Capacity of Thermomonospora alba XylA to impart thermostability in family F/10 chimeric xylanases.2001
Author(s)
Ahsan, M.M., Kaneko, S., Wang, Q., Yura, K., Go, M., Hayash, K.
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Journal Title
Enzyme Microb. Technol. 28(1)
Pages: 8-15
Description
「研究成果報告書概要(和文)」より
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[Journal Article] Mutational analysis of genes involved in pilus structure, motility and transformation competency in the unicellular motile cyanobacterium Synechocystis sp. PCC 6803.2001
Author(s)
Yoshihara, S., Geng.X.X., Okamoto, S., Yura, K., Murata, T., Go, M., Ohmori, M., Ikeuchi, M.
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Journal Title
Plant Cell Physiol 42(1)
Pages: 63-73
Description
「研究成果報告書概要(和文)」より
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[Journal Article] Dynamical transition of myoglobin in a crystal : comparative studies of X-ray crystallography and Mossbauer spectroscopy2001
Author(s)
Chong, S.-H., Joti, Y., Kidera.A., Go, N., Ostermann, A., Gassmann, A., Parak, F.
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Journal Title
European Biophysics J. 30(5)
Pages: 319-329
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Two KaiA-binding domains of cyanobacterial circadian clock protein KaiC2001
Author(s)
Taniguchi, Y., Yamagushi, A., Hijikata, A., lwasaki.H., Kamagata, K., Ishiura, M., Go, M., Kondo, T.
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Journal Title
FEBS Lett. 496(2-3)
Pages: 86-90
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Human ABCA1 contains a large amino-terminal extracellular domain homologous to an epitope of Sjogren's syndrome2001
Author(s)
Tanaka, A., Ikeda, Y., Abe-Dohmae, S., Arakawa.R., Sadanami, K., Kidera, A., Nakagawa, S., Nagase, T., Aoki, R., Kioka, N., Amachi, T., Yokoyama, S., Ueda, K.
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Journal Title
Biochem.Biophys.Res.Commun. 283 (5)
Pages: 1019-1025
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Capacity of Thermomonospora alba XylA to impart thermostability in family F/10 chimeric xylanases.2001
Author(s)
Ahsan, M.M., Kaneko, S., Wang, Q., Yura, K., Go, M., Hayash, K.
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Journal Title
Enzyme Microb.Technol. 28 (1)
Pages: 8-15
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Mutational analysis of genes involved in pilus structure, motility and transformation competency in the unicellular motile cyanobacterium Synechocystis sp. PCC 6803.2001
Author(s)
Yoshihara, S., Geng, X.X., Okamoto, S., Yura, K., Murata, T., Go.M., Ohmori, M., Ikeuchi, M.
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Journal Title
Plant Cell Physiol. 42 (1)
Pages: 63-73
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Ultrasonic. Properties of a Binary System of a Soluble Proein, a-Lactalbumin and Dimyristoyl Phosphatidylcholine Membrane.2000
Author(s)
Sakai, H., Imai, K., Tanaka, M., Sonoyama, M., Mitaku, S.
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Journal Title
Jpn. J. Appl. Phys. 39 (5B)
Pages: 2948-2949
Description
「研究成果報告書概要(和文)」より
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