STRategy for Interacting site Prediction
Scientific context
The first protein-protein interaction maps revealed a dense network of interactions with a high level of interconnections between nodes. Hence, phenotypes induced by the deletion of large regions of a gene bring about major perturbations that complicate the functional interpretation of a specific interaction. The functional dissection of an interaction network and the understanding of its molecular logic require a more local pertubation that breaks a specific interaction while keeping the rest of the network intact. For that purpose, one crucially needs new bioinformatic tools for predicting the site of the protein involved in the interaction. This is the aim of the STRIP project.
Teams involved
STRUCTURAL BIOINFORMATICS & NMR
Molecular Assemblies and Signaling Team
IbiTec-S/SB2SM/LBSR -CEA Saclay -91191 Gif sur Yvette Cedex
Raphaël GUEROIS, PhD
Françoise OCHSENBEIN, PhD
Emmanuelle BECKER
GENETICS & CELL BIOLOGY
DNA Metabolism and Genotoxic Stress Responses Laboratory
IbiTec-S/SBIGEM/LMARGE - CEA Saclay - 91191 Gif sur Yvette Cedex
Marie-Claude MARSOLIER-KERGOAT, PhD
Willy AUCHER, PhD
Emilie MA
Description of used services
- This site uses WebServices from the EBI:
Labarga A ., Valentin F., Andersson M. and Lopez R. (2007) Web Services at the European Bioinformatics Institute
Nucleic Acids Research Web Services Issue 2007.
abstract full-text HTML
- This site uses Netphos 2.0:
Blom, N., Gammeltoft, S., and Brunak, S.
Sequence- and structure-based prediction of eukaryotic protein phosphorylation sites.
Journal of Molecular Biology: 294(5): 1351-1362, 1999.
View the abstract. - This site uses Disphos 1.3:
Iakoucheva LM, Radivojac P, Brown CJ, O'Connor TR, Sikes JG, Obradovic Z, Dunker AK.
Intrinsic disorder and protein phosphorylation.
Nucleic Acids Research, 2004, 32 (3), 1037-1049. - This site uses NetphosK:
Blom N, Sicheritz-Ponten T, Gupta R, Gammeltoft S, Brunak S.
Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence.
Proteomics. 2004;4(6):1633-49. Review.
- This site uses Predphospho:
Kim JH, Lee J, Oh B, Kimm K, Koh I.
Prediction of phosphorylation sites using SVMs.
Bioinformatics. 2004;20(17):3179-84.
- This site uses Ppsp:
Xue Y, Li A, Wang L, Feng H, Yao X.
PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory.
BMC Bioinformatics. 2006;7:163.
- This site uses Scansite:
Obenauer JC, Cantley LC, Yaffe MB.
Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs.
Nucleic Acids Res. 2003;31(13):3635-41.
- This site uses Kinasephos:
H.D. Huang*, T.Y. Lee, S.W. Tseng, and J.T. Horng.
KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites
Nucleic Acids Research, 2005;33: W226-229.
