Prediction of protein-protein interactions from residue-pair interaction prediction

• Project/Area Number: 22500277
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Bioinformatics/Life informatics
• Research Institution: 独立行政法人医薬基盤研究所
• Principal Investigator: SHANDAR Ahmad 独立行政法人医薬基盤研究所, 創薬基盤研究部, 研究員 (80463298)
• Project Period (FY): 2010 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2012: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2011: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2010: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
• Keywords: バイオインフォマティクス / Prediction / Binding sites / Protein interactions / Evolutionary profiles / Partner-aware prediction / Neural network / Transfer of training / Protein complex / Residue-pair / Protein-protein interaction / Binding site / Protein function / Amino acids / Protein structure / protein function

Research Abstract

Methods for prediction of protein-protein interaction sites, interacting partners and for defining similarity between protein-protein complexes for classification have been developed. Core method is based on a neural network ensemble. Accuracy of the model is significantly improved by real-time training of models over query-specific data sets. Improvement in prediction accuracy of a protein P due to the presence of a protein Q in the training data is used as pair-wise similarity metric. A faster version of the model is developed for genomic scale application.

Research Products

• [Journal Article] Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins (2013)
  • Author(s): Nagarajan R, Ahmad S, GromihaM
  • Journal Title: Nucleic Acids Research Volume: (In Press)
  • Peer Reviewed
• [Journal Article] Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions (2013)
  • Author(s): Hutchins AP, Diez D, Takahashi Y, Ahmad S, Jauch R, Tremblay ML, Miranda-Saavedra D
  • Journal Title: Nucleic Acids Res Volume: 41(4) Pages: 2155-70
  • URL: http://dx.doi.org/10.1093/nar/gks1
  • Peer Reviewed
• [Journal Article] Distinct transcriptional regulatory modules underlie STAT3’s cell type-independent and cell type-specific functions (2013)
  • Author(s): Andrew Paul Hutchins, Diego Diez, Yoshiko Takahashi, Shandar Ahmad, Ralf Jauch, Michel Lucien Tremblay, Diego Miranda-Saavedra
  • Journal Title: Nucleic Acids Research Volume: 41 Issue: 4 Pages: 2155-2170
  • DOI: 10.1093/nar/gks1300
  • Peer Reviewed
• [Journal Article] Prediction and experimental validation of a putative non-consensus binding site for transcription factor STAT3 in Serum amyloid A gene promoter (2013)
  • Author(s): Prabha Tiwari, Lokesh P Tripathi, Teppei Nishikawa-Matsumura, Shandar Ahmad, Soken-Nakazawa J Song, Tomoyasu Isobe, Kenji Mizuguchi, Kazuyuki Yoshizaki
  • Journal Title: Biochimica et Biophysica Acta (BBA)-General Subjects Volume: 1830 Issue: 6 Pages: 3650-3655
  • DOI: 10.1016/j.bbagen.2013.01.024
  • Peer Reviewed
• [Journal Article] Prediction and experimental validation of a putative non-consensus binding site for transcription factor STAT3 in serum amyloid A gene promoter (2012)
  • Author(s): Tiwari P, Tripathi LP, Nishikawa-Matsumura T, Ahmad S, Song SN, Isobe T, Mizuguchi K, Yoshizaki K
  • Journal Title: Biochim Biophys Acta Volume: 1830(6) Pages: 3650-5
  • URL: http://dx.doi.org/10.1016/j.bbagen.2013.01.024
  • Peer Reviewed
• [Journal Article] Partner-aware prediction of interacting residues in protein-protein complexes from sequence data (2011)
  • Author(s): Ahmad S, Mizuguchi K
  • Journal Title: PLoS One Volume: 6(12)
  • Peer Reviewed
• [Journal Article] Analysis of electric moments of RNA-binding proteins: implications for mechanism and prediction (2011)
  • Author(s): Ahmad S, Sarai A
  • Journal Title: BMC Struct Biol Volume: 11 Pages: 8-8
  • URL: http://doi.org/10.1186/1472-6807-11-8
  • Peer Reviewed
• [Journal Article] Prediction of dinucleotide-specific RNA-binding sites in proteins (2011)
  • Author(s): Fernandez M, Kumagai Y, Standley DM, Sarai A, Mizuguchi K, Ahmad S
  • Journal Title: BMC Bioinformatics Volume: Nov 30
  • URL: http://doi.org/10.1186/1471-2105-12-S13-S5
  • Peer Reviewed
• [Journal Article] Residue propensities, discrimination and binding site prediction of adenine and guanine phosphates (2011)
  • Author(s): Firoz A, Malik A, Joplin KH, Ahmad Z, Jha V, Ahmad S
  • Journal Title: BMC Biochem Volume: 12 Pages: 20-20
  • URL: http://doi.org/10.1186/1471-2091-12-20
  • Peer Reviewed
• [Journal Article] Partner-aware prediction of interacting residues in protein-protein complexes from sequence data (2011)
  • Author(s): Shandar Ahmad, Kenji Mizuguchi
  • Journal Title: PLoS One Volume: VOL.6 Issue: 12 Pages: e29104-e29104
  • DOI: 10.1371/journal.pone.0029104
  • Peer Reviewed
• [Journal Article] Prediction of dinucleotide-specific RNA-binding Sites in Proteins (2011)
  • Author(s): M.Fernandez, Y.Kumagai, D.Standley, K.Mizuguchi, A.Sarai, S.Ahmad
  • Journal Title: BMC Bioiformatics Volume: 12 Issue: S13
  • DOI: 10.1186/1471-2105-12-s13-s5
  • Peer Reviewed
• [Journal Article] Residue propensities, discrimination and binding site prediction of adenine and guanine phosohates (2011)
  • Author(s): Ahmad Firoz, et al
  • Journal Title: BMC Biochemistry Volume: VOL.12 Issue: 1
  • DOI: 10.1186/1471-2091-12-20
  • Peer Reviewed
• [Journal Article] Analysis of electric moments of RNA-binding proteins : Implications for mechanism and prediction. (2011)
  • Author(s): Shandar Ahmad, Akinori Sarai
  • Journal Title: BMC Structural Biology Volume: 11
  • Peer Reviewed
• [Presentation] A meta-analysis of public microarray datasets to detect differential expression of heat shock proteins in children (2012)
  • Author(s): Shandar Ahmad
  • Organizer: Biomarker discovery conference
  • Place of Presentation: Shoal Bay, Australia
  • Year and Date: 2012-11-13
• [Presentation] A sliding-probe model for predicting partner aware protein-protein interaction sites (2012)
  • Author(s): Shandar Ahmad, Kenji Mizuguchi
  • Organizer: Genome Informatics Conference (GIW2012)
  • Place of Presentation: Taiwan
  • Year and Date: 2012-11-06
• [Presentation] A sliding-probe model for predicting partner aware protein-protein interaction sites (2012)
  • Author(s): Shandar Ahmad, Kenji Mizuguchi
  • Organizer: Geneome Informatics Conference (GIW2012)
  • Place of Presentation: Taiwan
• [Presentation] (1) A meta-analysis of public microarray datasets to detect differential expression of heat shock proteins in children (2012)
  • Author(s): Shandar Ahmad
  • Organizer: Biomarker discovery conference (BDC2012)
  • Place of Presentation: Shoal Bay, Australia
• [Presentation] Predicting Bio-molecular interactions in proteins and nucleic acids, International (2011)
  • Author(s): Shandar Ahmad
  • Organizer: Interdisciplinary science conference
  • Place of Presentation: Jamia Millia Islamia University, New Delhi, India (invited talk by Shandar Ahmad)
  • Year and Date: 2011-11-16
• [Presentation] Predicting Bio-molecular interactions in proteins and nucleic acids (2011)
  • Author(s): Shandar Ahmad
  • Organizer: International Interdisciplinary science conference
  • Place of Presentation: Jamia Millia Islamia University(インド、ニューデリ)(招待講演)
  • Year and Date: 2011-11-16
• [Presentation] Statistical analysis and prediction of kinked residue positions in helical membrane proteins (2010)
  • Author(s): Shandar Ahmad, Kenji Mizuguchi
  • Organizer: Japanese Society of Bioinformatics (JSBI) annual meeting 2010
  • Place of Presentation: Kyushu University, Fukuoka
  • Year and Date: 2010-11-13
• [Presentation] Michael Llamosa Fernandez, Akinori Sarai and Shandar Ahmad (2010)
  • Author(s): Kinase Inhibition Modeling by Proteochemometrics and Docking Analysis
  • Organizer: Intelligent Systems in Molecular Biology (ISMB 2010)
  • Place of Presentation: Boston, USA
  • Year and Date: 2010-07-12
• [Presentation] Sequence-to-structure prediction errors can reveal conformational flexibility in helical membrane proteins (2010)
  • Author(s): Shandar Ahmad, Hemjit Singh, Yogesh Paudel, Takaharu Mori, Yuji Sugita and Kenji Mizuguchi
  • Organizer: Intelligent Systems in Molecular Biology (ISMB 2010)
  • Place of Presentation: Boston, USA
  • Year and Date: 2010-07-11
• [Presentation] Prediction of dinucleotide-specific RNA-binding sites in proteins using sequence and evolutionary information (2010)
  • Author(s): Michael Llamosa Fernandez, Yutaro Kumagai, Daron Standley, Akinori Sarai, Kenji Mizuguchi, Shandar Ahmad
  • Organizer: Intelligent Systems in Molecular Biology (ISMB 2010)
  • Place of Presentation: Boston, USA
  • Year and Date: 2010-07-11
• [Remarks] 相互作用残基ペア及び単一の蛋白質相互作用部位を予測するウェブサーバーが開発され公開されている。さらなるソフトウェアとデータを公開予定。現在、投稿準備中。
  • URL: http://tardis.nibio.go.jp/netasa/ppipp/
• [Remarks]
  • URL: http://tardis.nibio.g.jp/netasa/ppipp/