Automated NMR signal assignment with self-learning system efficently using database

• Project/Area Number: 22570116
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: Osaka University
• Principal Investigator: KOBAYASHI Naohiro 大阪大学, たんぱく質研究所, 研究員 (80272160)
• Project Period (FY): 2010-04-01 – 2013-03-31
• Project Status: Completed (Fiscal Year 2013)
• Budget Amount: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000); Fiscal Year 2012: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2011: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000); Fiscal Year 2010: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
• Keywords: NMR / データベース / シグナル帰属 / 自動化 / 機械学習 / シグナル / 帰属 / GPU / 学習型 / 最適化

Research Abstract

NMR analysis provides not only structural information of macromolecules but also the important information about ligand interaction and dynamics which are related to drug design. In this project, a system including programs which automate NMR signal assignments. The performance that are expected from beginning of the project has been achieved a practical automated sequence specific assignments of backbone NMR signals. During this project, a quantitative assessment of consistency between NMR structure and assigned chemical shifts, and a method for automated identification of ordered region in NMR structure ensemble were published in the international journals. The programs developed in this project have been implemented in an integrate platform for NMR analysis and its demo version can be available from the web-site on the institute for protein research in University Osaka.

Research Products

• [Journal Article] A robust method for quantitative identification of ordered cores in an ensemble of biomolecular structures by non-linear multi-dimensional scaling using inter-atomic distance variance matrix (2014)
  • Author(s): Naohiro Kobayashi
  • Journal Title: J. Biomol. NMR Volume: 58巻 Issue: 1 Pages: 61-67
  • DOI: 10.1007/s10858-013-9805-z
  • Peer Reviewed
• [Journal Article] 1H, 13C, and 15N resonance assignments of the dsRBDs of mouse RNA helicase A (2013)
  • Author(s): Takashi Nagata T, Kengo Tsuda, Naohiro Kobayashi, Peter Guntert, Shigeyuki Yokoyama, and Yutaka Muto
  • Journal Title: Biomolecular NMR Assignment Volume: 7巻 Issue: 1 Pages: 69-72
  • DOI: 10.1007/s12104-012-9380-3
  • Peer Reviewed
• [Journal Article] ビッグデータ時代の生体高分子NMRデータベース、BioMagResBank (BMRB)その有効利用とわが国における現状 (2013)
  • Author(s): 小林直宏
  • Journal Title: 日本核磁気共鳴学会機関誌 Volume: 58巻 Pages: 121-124
  • Peer Reviewed
• [Journal Article] ビッグデータ時代の生体高分子ＮＭＲデータベース、BioMagResBank (BMRB) その有効利用とわが国における現状 (2013)
  • Author(s): 小林直宏
  • Journal Title: 日本核磁気共鳴学会機関誌 Volume: 4 Pages: 121-124
  • Peer Reviewed
• [Journal Article] Solution structure of the Splicing Factor Motif (SFM) of the human Prp18 protein (2012)
  • Author(s): He, F., Inoue, M., Kigawa, T., Takahashi, M., Kuwasako, K., Tsuda, K., Kobayashi, N., Terada, T., Shirouzu, M., Tanaka, A., Sugano, S., Guntert, P., Yokoyama, S., Muto, Y.
  • Journal Title: Proteins Volume: 80 Issue: 3 Pages: 968-974
  • DOI: 10.1002/prot.24003
  • Peer Reviewed
• [Journal Article] Structure of Musashi1 in a complex with target RNA : The role of aromatic stacking interactions (2012)
  • Author(s): Ohyama, T., Nagata, T., Tsuda, K., Kobayashi, N., Imai, T., Okano, H., Yamazaki, T. and Katahira, M
  • Journal Title: Nucleic Acids Res Volume: 10 Issue: 7 Pages: 3218-3231
  • DOI: 10.1093/nar/gkr1139
  • Peer Reviewed
• [Journal Article] Solution structures of the double-stranded RNA-binding domains from rna helicase A (2012)
  • Author(s): Takashi Nagata, Kengo Tsuda, Naohiro Kobayashi, Mikako Shirouzu, Takanori, Kigawa, Peter Guntert, Shigeyuki Yokoyama, and Yutaka Muto
  • Journal Title: Proteins Volume: 80巻 Issue: 6 Pages: 1699-1706
  • DOI: 10.1002/prot.24059
  • Peer Reviewed
• [Journal Article] NMR study of xenotropic murine leukemia virus-related virus protease in a complex with amprenavir (2012)
  • Author(s): Ayako Furukawa, Hideyasu Okamura, Ryo Morishita, Satoko Matsunaga, Naohiro Kobayashi, Takahisa Ikegami, Tsutomu Kodaki, Akifumi Takaori-Kondo, Ryo Akihide, Takashi Nagata, Masato Katahira
  • Journal Title: Biochem Biophys Res Commun. Volume: 24巻 Issue: 2 Pages: 284-289
  • DOI: 10.1016/j.bbrc.2012.07.083
  • NAID: 120004873605
  • Peer Reviewed
• [Journal Article] An automated system designed for large scale NMR data deposition and annotation : Application to over 600 assigned chemical shift data entries to the BioMagResBank from the RIKEN Structural Genomics/Proteomics Initiative internal database (2012)
  • Author(s): Naohiro Kobayashi, Yoko Harano, Naoya Tochio, Eiichi Nakatani, Takanori Kigawa, Shigeyuki Yokoyama, Steven Mading, Eldon L. Ulrich, John L. Markley, Hideo Akutsu and Toshimichi Fujiwara
  • Journal Title: J. Biomol. NMR Volume: 53巻 Issue: 4 Pages: 311-320
  • DOI: 10.1007/s10858-012-9641-6
  • Peer Reviewed
• [Journal Article] Structural insight into the interaction of ADP-ribose with the PARP WWE domains (2012)
  • Author(s): Fahu He, Kengo Tsuda, Mari Takahashi, Keiko Kuwasako, Takako Terada, Mikako Shirouzu, Satoru Watanabe, Takanori Kigawa, Naohiro Kobayashi, Peter Guntert, Shigeyuki Yokoyama, Yutaka Muto
  • Journal Title: FEBS Lett. Volume: 586巻 Issue: 21 Pages: 3858-3864
  • DOI: 10.1016/j.febslet.2012.09.009
  • Peer Reviewed
• [Journal Article] The NMR structure of FliK, the trigger for the switch of substrate specificity in the flagellar type III secretion appratus (2011)
  • Author(s): S.Mizuno, H.Amida, N.Kobayashi, S.Aizawa, S.Tate
  • Journal Title: J.Mol.Biol. Volume: 409 Issue: 4 Pages: 558-573
  • DOI: 10.1016/j.jmb.2011.04.008
  • Peer Reviewed
• [Journal Article] Structural basis for the dual RNA-recognition modes of human Tra2-β RRM (2011)
  • Author(s): Tsuda, K., Someya, T., Kuwasako, K., Takahashi, M., Fahu, H., Inoue, M., Harada, T., Watanabe, S., Terada, T., Kobayashi, N., Shirouzu, M., Kigawa, T., Tanaka, A., Sugano, S., Guntert, P., Yokoyama, S., Muto, Y.
  • Journal Title: Nucl.Acids Res. Volume: 39(4) Issue: 4 Pages: 1538-1553
  • DOI: 10.1093/nar/gkq854
  • Peer Reviewed
• [Journal Article] Structures of the first and second double-stranded RNA-binding domains of human TAR RNA-binding protein (2011)
  • Author(s): Seisuke Yamashita
  • Journal Title: Protein Sci. Volume: 20 Pages: 118-130
  • Peer Reviewed
• [Journal Article] Structural basis for the dual RNA-recognition modes of human Tra2-β RRM (2011)
  • Author(s): Kengo Tsuda
  • Journal Title: Nucleic Acids Res Volume: 39 Pages: 1538-1553
  • Peer Reviewed
• [Journal Article] Structural Insight into the Zinc Finger CW Domain as a Histone Modification Reader (2011)
  • Author(s): Fahu He
  • Journal Title: Structure Volume: 18 Pages: 1127-1139
  • Peer Reviewed
• [Presentation] 転写因子AML1に対して複数の結合部位を持つ高親和性RNAアプタマーの解析 (2013)
  • Author(s): 天野亮,野村祐介,永田崇,小林直宏,森瑶子,福永淳一,田中陽一郎,片平正人,中村義一,神津知子,坂本泰一
  • Organizer: 第36回日本分子生物学会年会
  • Place of Presentation: 神戸市
  • Year and Date: 2013-12-06
• [Presentation] Multi-site binding of high affinity aptamer against AML1 Runt domain (2013)
  • Author(s): 天野亮,野村祐介,永田崇,小林直宏,森瑶子,福永淳一,田中陽一郎,片平正人,中村義一,神津知子,坂本泰一
  • Organizer: 第40回国際核酸化学シンポジウム
  • Place of Presentation: 横浜市
  • Year and Date: 2013-12-03
• [Presentation] (2013)
  • Author(s): 永田崇,白川貴恵,小林直宏,始平堂弘和,片平正人,堀澤健一,土居信英,柳川弘志
  • Organizer: 第52回NMR討論会
  • Place of Presentation: 金沢市
  • Year and Date: 2013-11-12
• [Presentation] (2013)
  • Author(s): Naohiro Kobayashi
  • Organizer: International Conference on Structural Genomics 2013
  • Place of Presentation: 札幌市
  • Year and Date: 2013-07-29
• [Presentation] IVV法により取得した高選択的MDM2結合ペプチドによる MDM2: p53結合阻害の構造基盤 (2013)
  • Author(s): 永田 崇，白川貴恵，小林直宏，始平堂弘和，片平正人，堀澤健一，土居信英，柳川弘志
  • Organizer: 第52回NMR討論会
  • Place of Presentation: 金沢市
• [Presentation] 化学シフトデータベースを利用した高精度なNMR構造評価システム (2012)
  • Author(s): 小林直宏
  • Organizer: 第51回NMR討論会
  • Place of Presentation: 名古屋市
  • Year and Date: 2012-11-09
• [Presentation] 仮想化技術を用いたNMRデータの統合的解析環境 (2012)
  • Author(s): 小林直宏
  • Organizer: 第50回日本生物物理学会年会
  • Place of Presentation: 名古屋市
  • Year and Date: 2012-09-23
• [Presentation] 仮想化技術を活用した生体高分子の解析研究のすすめ (2012)
  • Author(s): 小林直宏
  • Organizer: 第12回蛋白質科学会年会
  • Place of Presentation: 名古屋市
  • Invited
• [Presentation] 仮想化技術による生体高分子NMR解析環境およびBMRBデータベースサーバーの統合化 (2012)
  • Author(s): 小林直宏
  • Organizer: トーゴーの日シンポジウム2012
  • Place of Presentation: 東京
  • Invited
• [Presentation] New server systems based on virtual computing for the database BMRB and MagRO-Tools for NMR analysis (2011)
  • Author(s): Noahiro Kobayashi
  • Organizer: 第50回NMR討論会記念国際シンポジウムISMAR2011
  • Place of Presentation: 横浜
  • Year and Date: 2011-11-16
• [Presentation] MagRO-Assign : A Tool for Automated Sequence Specific Assignment of Chemical Shifts for NMR Signals of Protein Backbone (2011)
  • Author(s): Noahiro Kobayashi
  • Organizer: EUROMAE2011
  • Place of Presentation: フランクフルト(ドイツ)
  • Year and Date: 2011-08-23
• [Presentation] NMRデータと構造アンサンブル、解析手法の基礎と応用 (2011)
  • Author(s): 小林直宏
  • Organizer: 新学術領域研究「天然変性タンパク質の分子認識と機能発現」第二回若手育成講習会
  • Place of Presentation: 大阪大学蛋白質研究所(大阪)(招待講演)
  • Year and Date: 2011-04-26
• [Presentation] New server systems based on virtual computing for the database BMRB and MagRO-Tools for NMR analysis (2011)
  • Author(s): Naohiro Kobayashi, Takeshi Iwata, Yoko Harano, Chojiro Kojima, Haruki Nakamura, Toshimichi Fujiwara
  • Organizer: 第50回記念NMR討論会国際シンポジウム
  • Place of Presentation: 横浜
• [Presentation] MagRO-Assign : a tool for automated sequence specific assignment of chemical shifts for NMR signals of protein backbone (2011)
  • Author(s): Naohiro Kobayashi, Ayako Furukawa, Soichiro Kitazawa, Takashi Nagata, Ryo Kitahara, Masato Katahira and Toshimichi Fujiwara
  • Organizer: EUROMAR2011
  • Place of Presentation: Frankfurt (Germany)
• [Presentation] オントロジー工学を利用したNMRデータ解析、評価およびデータベース登録を支援するツール、MagROシステムの開発 (2010)
  • Author(s): 小林直宏
  • Organizer: 第49回NMR討論会
  • Place of Presentation: タワーホール船堀(東京)
  • Year and Date: 2010-11-17
• [Presentation] A molecular viewer and tools for analysis and validation of NMR data and structure ensembles (2010)
  • Author(s): Naohiro Kobayashi
  • Organizer: XXIVth International Conference on Magnetic Resonance in Biological Systems (ICMRBS)
  • Place of Presentation: Cairns convention centre (Australia)
  • Year and Date: 2010-08-26
• [Presentation] 新しいデータ構造、データ評価法、自動解析技術によるNMR解析ツール群の開発 (2010)
  • Author(s): 小林直宏
  • Organizer: 蛋白研セミナー「実験と計算機科学で解明する蛋白質機能構造」
  • Place of Presentation: 大阪大学蛋白質研究所(大阪)(招待講演)
  • Year and Date: 2010-07-29
• [Remarks]
  • URL: http://bmrbdep.protein.osaka-u.ac.jp/en/nmrtoolbox/
• [Remarks] SPARTA Validation tool
  • URL: http://bmrbdep.pdbj.org/en/nmrtoolbox/sparta_validation_tool.html
• [Remarks] MagRO-NMRView
  • URL: http://bmrbdep.pdbj.org/en/nmrtoolbox/magro_nmrview.html
• [Remarks] FitRobot
  • URL: http://bmrbdep.pdbj.org/en/nmrtoolbox/fit_robot.html