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Volumn 6, Issue 10, 2011, Pages

Dompep-a general method for predicting modular domain-mediated protein-protein interactions

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BINDING AFFINITY; CALIBRATION; COMPUTER MODEL; COMPUTER PREDICTION; CONTROLLED STUDY; ENZYME SPECIFICITY; GENOME ANALYSIS; LIGAND BINDING; NUCLEOTIDE SEQUENCE; PREDICTION; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEOMICS; SRC HOMOLOGY DOMAIN; VALIDATION PROCESS; ANIMAL; ARTIFICIAL NEURAL NETWORK; BIOLOGY; GENOMICS; HUMAN; METABOLISM; METHODOLOGY; MOUSE; PDZ DOMAIN; PROTEIN ANALYSIS; PROTEIN TERTIARY STRUCTURE;

EID: 80053913061     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0025528     Document Type: Article
Times cited : (13)

References (45)
  • 4
    • 24044540256 scopus 로고    scopus 로고
    • Specificity and versatility of SH3 and other proline-recognition domains: structural basis and implications for cellular signal transduction
    • Li SS, (2005) Specificity and versatility of SH3 and other proline-recognition domains: structural basis and implications for cellular signal transduction. Biochem J 390: 641-653.
    • (2005) Biochem J , vol.390 , pp. 641-653
    • Li, S.S.1
  • 6
    • 70849112486 scopus 로고    scopus 로고
    • Cell signaling in space and time: where proteins come together and when they're apart
    • Scott JD, Pawson T, (2009) Cell signaling in space and time: where proteins come together and when they're apart. Science 326: 1220-1224.
    • (2009) Science , vol.326 , pp. 1220-1224
    • Scott, J.D.1    Pawson, T.2
  • 8
    • 0037453510 scopus 로고    scopus 로고
    • Assembly of cell regulatory systems through protein interaction domains
    • Pawson T, Nash P, (2003) Assembly of cell regulatory systems through protein interaction domains. Science 300: 445-452.
    • (2003) Science , vol.300 , pp. 445-452
    • Pawson, T.1    Nash, P.2
  • 9
    • 15644379801 scopus 로고    scopus 로고
    • Recognition of unique carboxyl-terminal motifs by distinct PDZ domains
    • Songyang Z, Fanning AS, Fu C, Xu J, Marfatia SM, et al. (1997) Recognition of unique carboxyl-terminal motifs by distinct PDZ domains. Science 275: 73-77.
    • (1997) Science , vol.275 , pp. 73-77
    • Songyang, Z.1    Fanning, A.S.2    Fu, C.3    Xu, J.4    Marfatia, S.M.5
  • 10
    • 0028540405 scopus 로고
    • Use of an Oriented Peptide Library to Determine the Optimal Substrates of Protein-Kinases
    • Zhou SY, Blechner S, Hoagland N, Hoekstra MF, Piwnicaworms H, et al. (1994) Use of an Oriented Peptide Library to Determine the Optimal Substrates of Protein-Kinases. Current Biology 4: 973-982.
    • (1994) Current Biology , vol.4 , pp. 973-982
    • Zhou, S.Y.1    Blechner, S.2    Hoagland, N.3    Hoekstra, M.F.4    Piwnicaworms, H.5
  • 11
    • 0027403027 scopus 로고
    • SH2 domains recognize specific phosphopeptide sequences
    • Songyang Z, Shoelson SE, Chaudhuri M, Gish G, Pawson T, et al. (1993) SH2 domains recognize specific phosphopeptide sequences. Cell 72: 767-778.
    • (1993) Cell , vol.72 , pp. 767-778
    • Songyang, Z.1    Shoelson, S.E.2    Chaudhuri, M.3    Gish, G.4    Pawson, T.5
  • 12
    • 42649123723 scopus 로고    scopus 로고
    • Defining the specificity space of the human SRC homology 2 domain
    • Huang H, Li L, Wu C, Schibli D, Colwill K, et al. (2008) Defining the specificity space of the human SRC homology 2 domain. Mol Cell Proteomics 7: 768-784.
    • (2008) Mol Cell Proteomics , vol.7 , pp. 768-784
    • Huang, H.1    Li, L.2    Wu, C.3    Schibli, D.4    Colwill, K.5
  • 14
    • 34250379613 scopus 로고    scopus 로고
    • Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening
    • Wu CG, Ma MHT, Brown KR, Geisler M, Li L, et al. (2007) Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening. Proteomics 7: 1775-1785.
    • (2007) Proteomics , vol.7 , pp. 1775-1785
    • Wu, C.G.1    Ma, M.H.T.2    Brown, K.R.3    Geisler, M.4    Li, L.5
  • 15
    • 34547127612 scopus 로고    scopus 로고
    • PDZ domain binding selectivity is optimized across the mouse proteome
    • Stiffler MA, Chen JR, Grantcharova VP, Lei Y, Fuchs D, et al. (2007) PDZ domain binding selectivity is optimized across the mouse proteome. Science 317: 364-369.
    • (2007) Science , vol.317 , pp. 364-369
    • Stiffler, M.A.1    Chen, J.R.2    Grantcharova, V.P.3    Lei, Y.4    Fuchs, D.5
  • 17
    • 33745185987 scopus 로고    scopus 로고
    • The human and mouse complement of SH2 domain proteins - Establishing the boundaries of phosphotyrosine signaling
    • Liu BA, Jablonowski K, Raina M, Arce M, Pawson T, et al. (2006) The human and mouse complement of SH2 domain proteins- Establishing the boundaries of phosphotyrosine signaling. Molecular Cell 22: 851-868.
    • (2006) Molecular Cell , vol.22 , pp. 851-868
    • Liu, B.A.1    Jablonowski, K.2    Raina, M.3    Arce, M.4    Pawson, T.5
  • 18
    • 0042622251 scopus 로고    scopus 로고
    • Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs
    • Obenauer JC, Cantley LC, Yaffe MB, (2003) Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res 31: 3635-3641.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3635-3641
    • Obenauer, J.C.1    Cantley, L.C.2    Yaffe, M.B.3
  • 19
    • 45549090122 scopus 로고    scopus 로고
    • Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach
    • Li L, Wu C, Huang H, Zhang K, Gan J, et al. (2008) Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach. Nucleic Acids Res 36: 3263-3273.
    • (2008) Nucleic Acids Res , vol.36 , pp. 3263-3273
    • Li, L.1    Wu, C.2    Huang, H.3    Zhang, K.4    Gan, J.5
  • 20
    • 52649145895 scopus 로고    scopus 로고
    • GPS 2.0, a Tool to Predict Kinase-specific Phosphorylation Sites in Hierarchy
    • Xue Y, Ren J, Gao X, Jin C, Wen L, et al. (2008) GPS 2.0, a Tool to Predict Kinase-specific Phosphorylation Sites in Hierarchy. Mol Cell Proteomics 7: 1598-1608.
    • (2008) Mol Cell Proteomics , vol.7 , pp. 1598-1608
    • Xue, Y.1    Ren, J.2    Gao, X.3    Jin, C.4    Wen, L.5
  • 21
    • 37849047943 scopus 로고    scopus 로고
    • Prediction of kinase-specific phosphorylation sites with sequence features by a log-odds ratio approach
    • Li T, Li F, Zhang X, (2008) Prediction of kinase-specific phosphorylation sites with sequence features by a log-odds ratio approach. Proteins 70: 404-414.
    • (2008) Proteins , vol.70 , pp. 404-414
    • Li, T.1    Li, F.2    Zhang, X.3
  • 22
    • 23144434356 scopus 로고    scopus 로고
    • KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites
    • Huang HD, Lee TY, Tzeng SW, Horng JT, (2005) KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites. Nucleic Acids Res 33: W226-229.
    • (2005) Nucleic Acids Res , vol.33
    • Huang, H.D.1    Lee, T.Y.2    Tzeng, S.W.3    Horng, J.T.4
  • 23
    • 8844219516 scopus 로고    scopus 로고
    • Prediction of phosphorylation sites using SVMs
    • Kim JH, Lee J, Oh B, Kimm K, Koh I, (2004) Prediction of phosphorylation sites using SVMs. Bioinformatics 20: 3179-3184.
    • (2004) Bioinformatics , vol.20 , pp. 3179-3184
    • Kim, J.H.1    Lee, J.2    Oh, B.3    Kimm, K.4    Koh, I.5
  • 26
    • 0034724569 scopus 로고    scopus 로고
    • SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family
    • Brannetti B, Via A, Cestra G, Cesareni G, Citterich MH, (2000) SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family. Journal of Molecular Biology 298: 313-328.
    • (2000) Journal of Molecular Biology , vol.298 , pp. 313-328
    • Brannetti, B.1    Via, A.2    Cestra, G.3    Cesareni, G.4    Citterich, M.H.5
  • 27
    • 66149146342 scopus 로고    scopus 로고
    • Characterization of Domain-Peptide Interaction Interface: A Generic Structure-based Model to Decipher the Binding Specificity of SH3 Domains
    • Hou T, Xu Z, Zhang W, McLaughlin WA, Case DA, et al. (2009) Characterization of Domain-Peptide Interaction Interface: A Generic Structure-based Model to Decipher the Binding Specificity of SH3 Domains. Mol Cell Proteomics 8: 639-649.
    • (2009) Mol Cell Proteomics , vol.8 , pp. 639-649
    • Hou, T.1    Xu, Z.2    Zhang, W.3    McLaughlin, W.A.4    Case, D.A.5
  • 28
    • 33746285302 scopus 로고    scopus 로고
    • An integrated machine learning system to computationally screen protein databases for protein binding peptide ligands
    • Zhang L, Shao C, Zheng D, Gao Y, (2006) An integrated machine learning system to computationally screen protein databases for protein binding peptide ligands. Mol Cell Proteomics 5: 1224-1232.
    • (2006) Mol Cell Proteomics , vol.5 , pp. 1224-1232
    • Zhang, L.1    Shao, C.2    Zheng, D.3    Gao, Y.4
  • 31
    • 0034924493 scopus 로고    scopus 로고
    • SWISS-PROT: connecting biomolecular knowledge via a protein database
    • Gasteiger E, Jung E, Bairoch A, (2001) SWISS-PROT: connecting biomolecular knowledge via a protein database. Curr Issues Mol Biol 3: 47-55.
    • (2001) Curr Issues Mol Biol , vol.3 , pp. 47-55
    • Gasteiger, E.1    Jung, E.2    Bairoch, A.3
  • 32
    • 77953853695 scopus 로고    scopus 로고
    • Loops govern SH2 domain specificity by controlling access to binding pockets
    • Kaneko T, Huang H, Zhao B, Li L, Liu H, et al. (2010) Loops govern SH2 domain specificity by controlling access to binding pockets. Sci Signal 3: ra34.
    • (2010) Sci Signal , vol.3
    • Kaneko, T.1    Huang, H.2    Zhao, B.3    Li, L.4    Liu, H.5
  • 33
    • 78149333493 scopus 로고    scopus 로고
    • SH2 domains recognize contextual peptide sequence information to determine selectivity
    • Liu BA, Jablonowski K, Shah EE, Engelmann BW, Jones RB, et al. (2010) SH2 domains recognize contextual peptide sequence information to determine selectivity. Mol Cell Proteomics 9: 2391-2404.
    • (2010) Mol Cell Proteomics , vol.9 , pp. 2391-2404
    • Liu, B.A.1    Jablonowski, K.2    Shah, E.E.3    Engelmann, B.W.4    Jones, R.B.5
  • 34
    • 0028354446 scopus 로고
    • Nuclear magnetic resonance structure of an SH2 domain of phospholipase C-gamma 1 complexed with a high affinity binding peptide
    • Pascal SM, Singer AU, Gish G, Yamazaki T, Shoelson SE, et al. (1994) Nuclear magnetic resonance structure of an SH2 domain of phospholipase C-gamma 1 complexed with a high affinity binding peptide. Cell 77: 461-472.
    • (1994) Cell , vol.77 , pp. 461-472
    • Pascal, S.M.1    Singer, A.U.2    Gish, G.3    Yamazaki, T.4    Shoelson, S.E.5
  • 35
    • 21244439157 scopus 로고    scopus 로고
    • hScrib interacts with ZO-2 at the cell-cell junctions of epithelial cells
    • Metais JY, Navarro C, Santoni MJ, Audebert S, Borg JP, (2005) hScrib interacts with ZO-2 at the cell-cell junctions of epithelial cells. FEBS Lett 579: 3725-3730.
    • (2005) FEBS Lett , vol.579 , pp. 3725-3730
    • Metais, J.Y.1    Navarro, C.2    Santoni, M.J.3    Audebert, S.4    Borg, J.P.5
  • 36
    • 33645132429 scopus 로고    scopus 로고
    • Human scribble, a novel tumor suppressor identified as a target of high-risk HPV E6 for ubiquitin-mediated degradation, interacts with adenomatous polyposis coli
    • Takizawa S, Nagasaka K, Nakagawa S, Yano T, Nakagawa K, et al. (2006) Human scribble, a novel tumor suppressor identified as a target of high-risk HPV E6 for ubiquitin-mediated degradation, interacts with adenomatous polyposis coli. Genes Cells 11: 453-464.
    • (2006) Genes Cells , vol.11 , pp. 453-464
    • Takizawa, S.1    Nagasaka, K.2    Nakagawa, S.3    Yano, T.4    Nakagawa, K.5
  • 37
    • 33748923940 scopus 로고    scopus 로고
    • Scribble associates with two polarity proteins, Lgl2 and Vangl2, via distinct molecular domains
    • Kallay LM, McNickle A, Brennwald PJ, Hubbard AL, Braiterman LT, (2006) Scribble associates with two polarity proteins, Lgl2 and Vangl2, via distinct molecular domains. J Cell Biochem 99: 647-664.
    • (2006) J Cell Biochem , vol.99 , pp. 647-664
    • Kallay, L.M.1    McNickle, A.2    Brennwald, P.J.3    Hubbard, A.L.4    Braiterman, L.T.5
  • 38
    • 22344441238 scopus 로고    scopus 로고
    • The tumor suppressor Scrib interacts with the zyxin-related protein LPP, which shuttles between cell adhesion sites and the nucleus
    • Petit MM, Meulemans SM, Alen P, Ayoubi TA, Jansen E, et al. (2005) The tumor suppressor Scrib interacts with the zyxin-related protein LPP, which shuttles between cell adhesion sites and the nucleus. BMC Cell Biol 6: 1.
    • (2005) BMC Cell Biol , vol.6 , pp. 1
    • Petit, M.M.1    Meulemans, S.M.2    Alen, P.3    Ayoubi, T.A.4    Jansen, E.5
  • 39
    • 2642547462 scopus 로고    scopus 로고
    • Mammalian Scribble forms a tight complex with the betaPIX exchange factor
    • Audebert S, Navarro C, Nourry C, Chasserot-Golaz S, Lecine P, et al. (2004) Mammalian Scribble forms a tight complex with the betaPIX exchange factor. Curr Biol 14: 987-995.
    • (2004) Curr Biol , vol.14 , pp. 987-995
    • Audebert, S.1    Navarro, C.2    Nourry, C.3    Chasserot-Golaz, S.4    Lecine, P.5
  • 40
    • 13244289881 scopus 로고    scopus 로고
    • Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins
    • Diella F, Cameron S, Gemund C, Linding R, Via A, et al. (2004) Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinformatics 5: 79.
    • (2004) BMC Bioinformatics , vol.5 , pp. 79
    • Diella, F.1    Cameron, S.2    Gemund, C.3    Linding, R.4    Via, A.5
  • 42
    • 70349526350 scopus 로고    scopus 로고
    • Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases
    • Tan CS, Bodenmiller B, Pasculescu A, Jovanovic M, Hengartner MO, et al. (2009) Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases. Sci Signal 2: ra39.
    • (2009) Sci Signal , vol.2
    • Tan, C.S.1    Bodenmiller, B.2    Pasculescu, A.3    Jovanovic, M.4    Hengartner, M.O.5
  • 43
    • 41149167511 scopus 로고    scopus 로고
    • Network medicine
    • Pawson T, Linding R, (2008) Network medicine. FEBS letters 582: 1266-1270.
    • (2008) FEBS Letters , vol.582 , pp. 1266-1270
    • Pawson, T.1    Linding, R.2
  • 44
    • 0002714543 scopus 로고    scopus 로고
    • Making Large-Scale SVM Learning Practical
    • In: Schölkopf B, Burges C, Smola A, editors, Cambridge, USA, MIT Press
    • Joachims T, (1999) Making Large-Scale SVM Learning Practical. In: Schölkopf B, Burges C, Smola A, editors. Advances in Kernel Methods- Support Vector Learning Cambridge, USA MIT Press.
    • (1999) Advances in Kernel Methods - Support Vector Learning
    • Joachims, T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.