SH3-Hunter: Discovery of SH3 domain interaction sites in proteins

Nucleic Acids Research

Volumn 35, Issue SUPPL.2, 2007, Pages

  Ferraro, Enrico ^a   Peluso, Daniele ^a   Via, Allegra ^a   Ausiello, Gabriele ^a   Helmer Citterich, Manuela ^a  

^a UNIVERSITY OF ROME TOR VERGATA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE; PEPTIDE LIBRARY;

AMINO ACID SEQUENCE; ARTICLE; ARTIFICIAL NEURAL NETWORK; BINDING SITE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; METHODOLOGY; PROTEIN BINDING; PROTEIN MOTIF; PROTEIN TERTIARY STRUCTURE; SENSITIVITY AND SPECIFICITY; SRC HOMOLOGY DOMAIN;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; BINDING SITES; COMPUTATIONAL BIOLOGY; HUMANS; MODELS, MOLECULAR; NEURAL NETWORKS (COMPUTER); PEPTIDE LIBRARY; PEPTIDES; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; SENSITIVITY AND SPECIFICITY; SRC HOMOLOGY DOMAINS;

EID: 34547571029     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm296     Document Type: Article

References (15)

1. Masumi, A., Aizaki, H., Suzuki, T., DuHadaway, J.B., Prendergast, G.C., Komuro, K. and Fukazawa, H. (2005) Reduction of hepatitis C virus NS5A phosphorylation through its interaction with amphiphysin II. Biochem. Biophys. Res. Commun., 366, 572-578.
2. Stamenova, S.D., French, M.E., He, Y., Francis, S.A., Kramer, Z.B. and Hicke, L. (2007) Ubiquitins binds to and regulates a subset of SH3 domains. Mol. Cell, 25, 273-284.
3. Kay, B.K., Williamson, M.P. and Sudol, M. (2000) The importance of being proline: The interaction of proline-rich motifs in signaling proteins with their cognate domains. FASEB J., 14, 231-241.
4. Landgraf, C., Panni, S., Montecchi-Palazzi, L., Castagnoli, L., Schneider-Mergener, J., Volkmer-Engert, R. and Cesareni, G. (2004) Protein interaction networks by proteome peptide scanning. PLoS Biol., 2, 94-103.
5. You, X., Nguyen, A.W., Jabaiah, A., Sheff, M.A., Thorn, K.S. and Daugherty, P.S. (2006) Intracellular protein interaction mapping with FRET hybrids. Proc. Natl Acad. Sci. USA, 103, 18458-18463.
6. Hou, T., Chen, K., McLaughlin, W.A., Lu, B. and Wang, W. (2006) Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain. PLoS Comput. Biol., 2, e1.
7. Lehrach, W.P., Husmeier, D. and Williams, C.K. (2006) A regularized discriminative model for the prediction of protein-protein interactions. Bioinformatics, 22, 532-540.
8. Ferraro, E., Via, A., Ausiello, G. and Helmer-Citterich, M. (2006) A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity. Bioinformatics, 22, 2333-2339.
9. Mayer, B.J. (2001) SH3 domains: Complexity in moderation. J. Cell Sci., 114, 1253-1263.
10. Musacchio, A. (2002) How SH3 domains recognize proline. Adv. Protein Chem., 61, 211-268.
11. Brannetti, B., Via, A., Cestra, G., Cesareni, G. and Helmer-citterich, M. (2000) SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family. J. Mol. Biol., 298, 313-328.
12. Cesareni, G., Panni, S., Nardelli, G. and Castagnoli, L. (2001) Can we infer peptide recognition specificity mediated by SH3 domains? FEBS Letters, 513, 38-44.
13. Tong, A.H., Drees, B., Nardelli, G., Bader, G.D., Brannetti, B., Castagnoli, L., Evangelista, M., Ferracuti, S., Nelson, B., Paoluzi, S., Quondam, M., Zucconi, A., Hogue, C.W., Fields, S., Boone, C. and Cesareni, G. (2002) A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science, 295, 321-324.
14. Bishop, C.M. (1995) Neural Networks for Pattern Recognition Oxford University Press.
15. Higgins, D., Thompson, J., Gibson, T., Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.