In-silico prediction of active comformations by machine learning

• Project/Area Number: 21680025
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Single-year Grants
• Research Field: Bioinformatics/Life informatics
• Research Institution: National Institute of Advanced Industrial Science and Technology
• Principal Investigator: TSUDA Koji 独立行政法人産業技術総合研究所, 生命情報工学研究センター, 主任研究員 (90357517)
• Project Period (FY): 2009 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥19,890,000 (Direct Cost: ¥15,300,000、Indirect Cost: ¥4,590,000); Fiscal Year 2012: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000); Fiscal Year 2011: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000); Fiscal Year 2010: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000); Fiscal Year 2009: ¥8,450,000 (Direct Cost: ¥6,500,000、Indirect Cost: ¥1,950,000)
• Keywords: 機械学習 / 生体分子 / 生理活性

Research Abstract

The amount of protein 3D structure information is ever increasing as the number of registered proteins in Protein Data Bank (PDB) exceeded 70,000. To extract functional information, we developed a fast all pairs similarity search a

Research Products

• [Journal Article] PoSSuM: a Database of Similar Protein-Ligand Binding and Putative Pockets (2012)
  • Author(s): J. Ito, Y. Tabei, K. Shimizu, K. Tsuda and K. Tomii
  • Journal Title: Nucleic Acids Research Volume: 40 Issue: D1 Pages: D541-D548
  • DOI: 10.1093/nar/gkr1130
  • Peer Reviewed
• [Journal Article] PDB-scale Analysis of Known and Putative Ligand-binding Sites with Structural Sketches (2012)
  • Author(s): J. Ito, Y. Tabei, K. Shimizu, K. Tomii and K. Tsuda
  • Journal Title: Proteins Volume: 80 Issue: 3 Pages: 747-763
  • DOI: 10.1002/prot.23232
  • Peer Reviewed
• [Journal Article] SlideSort: All Pairs Similarity Search for Short Reads (2011)
  • Author(s): K. Shimizu and K. Tsuda
  • Journal Title: Bioinformatics Volume: 27 Issue: 4 Pages: 464-470
  • DOI: 10.1093/bioinformatics/btq677
  • Peer Reviewed
• [Journal Article] SketchSort: Fast All Pairs Similarity Search for Large Databases of Molecular Fingerprints (2011)
  • Author(s): Y. Tabei and K. Tsuda
  • Journal Title: Molecular Informatics Volume: 30 Issue: 9 Pages: 801-807
  • DOI: 10.1002/minf.201100050
  • Peer Reviewed
• [Journal Article] SlideSort : All Pairs Similarity Search for Short Reads (2011)
  • Author(s): Kana Shimizu, Koji Tsuda
  • Journal Title: Bioinformatics Volume: 27 Pages: 464-470
  • Peer Reviewed
• [Journal Article] Multi-Way Set Enumeration in Weight Tensors (2011)
  • Author(s): Elisabeth Georgii, Koji Tsuda, Bernhard Schoelkopf
  • Journal Title: Machine Learning Volume: 82 Pages: 123-155
  • Peer Reviewed
• [Journal Article] Mining Significant Substructure Pairs for Interpreting Polypharmacology in Drug-Target Network (2011)
  • Author(s): Ichigaku Takigawa, Koji Tsuda, Hiroshi Mamitsuka
  • Journal Title: Plos One Volume: 6
  • NAID: 120002949745
  • Peer Reviewed
• [Journal Article] Reaction Graph Kernels Predict EC Numbers of Unknown Enzymatic Reactions in Plant Secondary Metabolism (2010)
  • Author(s): H.Saigo, M.Hattori, H.Kashima, K.Tsuda
  • Journal Title: BMC Bioinformatics 11, Suppl.1
  • Peer Reviewed
• [Journal Article] Efficiently Finding Genome-wide Three-way Interactions from Transcript and Genotype-Data (2009)
  • Author(s): M.Kayano, I.Takigawa, M.Shiga, K.Tsuda, H.Mamitsuka
  • Journal Title: Bioinformatics 25 Pages: 2735-2743
  • Peer Reviewed
• [Journal Article] Submodularity Cuts and Applications (2009)
  • Author(s): Y.Kawahara, K.Nagano, K.Tsuda, J.Bilmes
  • Journal Title: Advances in Neural Information Processing Systems 22 Pages: 916-924
  • Peer Reviewed
• [Presentation] Possum: A Database for Predicting Protein-Ligand Interactions (2012)
  • Author(s): K. Tomii, J. Ito, Y . Tabei, K. Shimizu, K.Tsuda
  • Organizer: 生命医薬情報学連合大会
  • Place of Presentation: 東京都、タワーホール船堀
  • Year and Date: 2012-10-14
• [Presentation] Junichi Ito (2012)
  • Author(s): Kentaro Tomii
  • Organizer: Koji Tsuda
  • Place of Presentation: 東京都、タワーホール船堀
• [Remarks]
  • URL: http://possum.cbrc.jp/PoSSuM/
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