Nucleic Acids Research, 2003, Vol. 31, No. 13 3635-3641
© 2003 Oxford University Press
Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs
Center for Cancer Research, E18-580, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA 1 Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA, USA
*To whom correspondence should be addressed. Tel: +1 6174522103; Fax: +1 6174524978; Email: myaffe{at}mit.edu
Scansite identifies short protein sequence motifs that are recognized by modular signaling domains, phosphorylated by protein Ser/Thr- or Tyr-kinases or mediate specific interactions with protein or phospholipid ligands. Each sequence motif is represented as a position-specific scoring matrix (PSSM) based on results from oriented peptide library and phage display experiments. Predicted domain-motif interactions from Scansite can be sequentially combined, allowing segments of biological pathways to be constructed in silico. The current release of Scansite, version 2.0, includes 62 motifs characterizing the binding and/or substrate specificities of many families of Ser/Thr- or Tyr-kinases, SH2, SH3, PDZ, 14-3-3 and PTB domains, together with signature motifs for PtdIns(3,4,5)P3-specific PH domains. Scansite 2.0 contains significant improvements to its original interface, including a number of new generalized user features and significantly enhanced performance. Searches of all SWISS-PROT, TrEMBL, Genpept and Ensembl protein database entries are now possible with run times reduced by 
60% when compared with Scansite version 1.0. Scansite 2.0 allows restricted searching of species-specific proteins, as well as isoelectric point and molecular weight sorting to facilitate comparison of predictions with results from two-dimensional gel electrophoresis experiments. Support for user-defined motifs has been increased, allowing easier input of user-defined matrices and permitting user-defined motifs to be combined with pre-compiled Scansite motifs for dual motif searching. In addition, a new series of Sequence Match programs for non-quantitative user-defined motifs has been implemented. Scansite is available via the World Wide Web at http://scansite.mit.edu.
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R. Linding, L. J. Jensen, A. Pasculescu, M. Olhovsky, K. Colwill, P. Bork, M. B. Yaffe, and T. Pawson NetworKIN: a resource for exploring cellular phosphorylation networks Nucleic Acids Res., January 11, 2008; 36(suppl_1): D695 - D699. [Abstract] [Full Text] [PDF]
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W. Gong, D. Zhou, Y. Ren, Y. Wang, Z. Zuo, Y. Shen, F. Xiao, Q. Zhu, A. Hong, X. Zhou, et al. PepCyber:P~PEP: a database of human protein protein interactions mediated by phosphoprotein-binding domains Nucleic Acids Res., January 11, 2008; 36(suppl_1): D679 - D683. [Abstract] [Full Text] [PDF]
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H. Dinkel and H. Sticht A computational strategy for the prediction of functional linear peptide motifs in proteins Bioinformatics, December 15, 2007; 23(24): 3297 - 3303. [Abstract] [Full Text] [PDF]
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M. P. Stokes, J. Rush, J. MacNeill, J. M. Ren, K. Sprott, J. Nardone, V. Yang, S. A. Beausoleil, S. P. Gygi, M. Livingstone, et al. Profiling of UV-induced ATM/ATR signaling pathways PNAS, December 11, 2007; 104(50): 19855 - 19860. [Abstract] [Full Text] [PDF]
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R. W. Anantha, V. M. Vassin, and J. A. Borowiec Sequential and Synergistic Modification of Human RPA Stimulates Chromosomal DNA Repair J. Biol. Chem., December 7, 2007; 282(49): 35910 - 35923. [Abstract] [Full Text] [PDF]
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J.-S. Kim, B. A. Diebold, B. M. Babior, U. G. Knaus, and G. M. Bokoch Regulation of Nox1 Activity via Protein Kinase A-mediated Phosphorylation of NoxA1 and 14-3-3 Binding J. Biol. Chem., November 30, 2007; 282(48): 34787 - 34800. [Abstract] [Full Text] [PDF]
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 J. Y. Delgado, M. Coba, C. N. G. Anderson, K. R. Thompson, E. E. Gray, C. L. Heusner, K. C. Martin, S. G. N. Grant, and T. J. O'Dell NMDA Receptor Activation Dephosphorylates AMPA Receptor Glutamate Receptor 1 Subunits at Threonine 840 J. Neurosci., November 28, 2007; 27(48): 13210 - 13221. [Abstract] [Full Text] [PDF]
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M. W. Mayhew, E. D. Jeffery, N. E. Sherman, K. Nelson, J. M. Polefrone, S. J. Pratt, J. Shabanowitz, J. T. Parsons, J. W. Fox, D. F. Hunt, et al. Identification of phosphorylation sites in betaPIX and PAK1 J. Cell Sci., November 15, 2007; 120(22): 3911 - 3918. [Full Text] [PDF]
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Y. Zhang, V. Brovkovych, S. Brovkovych, F. Tan, B.-S. Lee, T. Sharma, and R. A. Skidgel Dynamic Receptor-dependent Activation of Inducible Nitric-oxide Synthase by ERK-mediated Phosphorylation of Ser745 J. Biol. Chem., November 2, 2007; 282(44): 32453 - 32461. [Abstract] [Full Text] [PDF]
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J. E. Hutti, B. E. Turk, J. M. Asara, A. Ma, L. C. Cantley, and D. W. Abbott I{kappa}B Kinase {beta} Phosphorylates the K63 Deubiquitinase A20 To Cause Feedback Inhibition of the NF-{kappa}B Pathway Mol. Cell. Biol., November 1, 2007; 27(21): 7451 - 7461. [Abstract] [Full Text] [PDF]
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C. Medina-Palazon, H. Gruffat, F. Mure, O. Filhol, V. Vingtdeux-Didier, H. Drobecq, C. Cochet, N. Sergeant, A. Sergeant, and E. Manet Protein Kinase CK2 Phosphorylation of EB2 Regulates Its Function in the Production of Epstein-Barr Virus Infectious Viral Particles J. Virol., November 1, 2007; 81(21): 11850 - 11860. [Abstract] [Full Text] [PDF]
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 L. Cao, K. Yu, C. Banh, V. Nguyen, A. Ritz, B. J. Raphael, Y. Kawakami, T. Kawakami, and A. R. Salomon Quantitative Time-Resolved Phosphoproteomic Analysis of Mast Cell Signaling J. Immunol., November 1, 2007; 179(9): 5864 - 5876. [Abstract] [Full Text] [PDF]
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E. Com, C. Lagadec, A. Page, I. El Yazidi-Belkoura, C. Slomianny, A. Spencer, D. Hammache, B. B. Rudkin, and H. Hondermarck Nerve Growth Factor Receptor TrkA Signaling in Breast Cancer Cells Involves Ku70 to Prevent Apoptosis Mol. Cell. Proteomics, November 1, 2007; 6(11): 1842 - 1854. [Abstract] [Full Text] [PDF]
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F. Causeret, T. Jacobs, M. Terao, O. Heath, M. Hoshino, and M. Nikolic Neurabin-I Is Phosphorylated by Cdk5: Implications for Neuronal Morphogenesis and Cortical Migration Mol. Biol. Cell, November 1, 2007; 18(11): 4327 - 4342. [Abstract] [Full Text] [PDF]
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P. Uvarov, A. Ludwig, M. Markkanen, P. Pruunsild, K. Kaila, E. Delpire, T. Timmusk, C. Rivera, and M. S. Airaksinen A Novel N-terminal Isoform of the Neuron-specific K-Cl Cotransporter KCC2 J. Biol. Chem., October 19, 2007; 282(42): 30570 - 30576. [Abstract] [Full Text] [PDF]
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D. A. Alvarez-Arias and K. S. Campbell Protein Kinase C Regulates Expression and Function of Inhibitory Killer Cell Ig-Like Receptors in NK Cells J. Immunol., October 15, 2007; 179(8): 5281 - 5290. [Abstract] [Full Text] [PDF]
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 J. M. Stommel, A. C. Kimmelman, H. Ying, R. Nabioullin, A. H. Ponugoti, R. Wiedemeyer, A. H. Stegh, J. E. Bradner, K. L. Ligon, C. Brennan, et al. Coactivation of Receptor Tyrosine Kinases Affects the Response of Tumor Cells to Targeted Therapies Science, October 12, 2007; 318(5848): 287 - 290. [Abstract] [Full Text] [PDF]
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E. Sjottem, C. Rekdal, G. Svineng, S. S. Johnsen, H. Klenow, R. D. Uglehus, and T. Johansen The ePHD protein SPBP interacts with TopBP1 and together they co-operate to stimulate Ets1-mediated transcription Nucleic Acids Res., October 8, 2007; 35(19): 6648 - 6662. [Abstract] [Full Text] [PDF]
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