Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs.

@article{citeulike:2402373, abstract = {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)P(3)-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 approximately 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.}, address = {Center for Cancer Research, E18-580, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.}, author = {Obenauer, J. C. and Cantley, L. C. and Yaffe, M. B. }, citeulike-article-id = {2402373}, doi = {10.1093/nar/gkg584}, issn = {1362-4962}, journal = {Nucleic Acids Res}, keywords = {algorithm, amino-acid, analysis, article-nar, article-predikin, binding, database, internet, motifs, phosphorylation, protein, proteome, sequence, signal, sites, software, structure, transduction}, month = {July}, number = {13}, pages = {3635--3641}, posted-at = {2008-04-24 16:16:06}, priority = {2}, title = {Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs.}, url = {http://dx.doi.org/10.1093/nar/gkg584}, volume = {31}, year = {2003} }

TY - JOUR ID - citeulike:2402373 L3 - citeulike-article-id:2402373 TI - Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. JF - Nucleic Acids Res VL - 31 IS - 13 SP - 3635 EP - 3641 AD - Center for Cancer Research, E18-580, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA. SN - 1362-4962 N2 - 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)P(3)-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 approximately 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. KW - algorithm KW - amino-acid KW - analysis KW - article-nar KW - article-predikin KW - binding KW - database KW - internet KW - motifs KW - phosphorylation KW - protein KW - proteome KW - sequence KW - signal KW - sites KW - software KW - structure KW - transduction AU - Obenauer, JC AU - Cantley, LC AU - Yaffe, MB PY - 2003/07/01/ UR - http://dx.doi.org/10.1093/nar/gkg584 ER -