iELM-a web server to explore short linear motif-mediated interactions

Nucleic Acids Research

Volumn 40, Issue W1, 2012, Pages

  Weatheritt, Robert J ^a   Jehl, Peter ^a   Dinkel, Holger ^a   Gibson, Toby J ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COMPLEX FORMATION; COMPUTER GRAPHICS; COMPUTER PROGRAM; EUKARYOTE; INTERNET; PREDICTION; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEOMICS; SHORT LINEAR MOTIF; WEB SERVER;

ALGORITHMS; INTERNET; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN INTERACTION MAPPING; PROTEOMICS; SOFTWARE; USER-COMPUTER INTERFACE;

EUKARYOTA;

EID: 84864465529     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks444     Document Type: Article

References (33)

1. Weatheritt, R.J., Luck, K., Petsalaki, E., Davey, N.E. and Gibson, T.J. (2012) The identification of short linear motifmediated interfaces within the human interactome. Bioinformatics, 28, 976-982.
2. Gibson, T.J. (2009) Cell regulation: determined to signal discrete cooperation. Trends Biochem. Sci., 34, 471-482.
3. Dinkel, H., Michael, S., Weatheritt, R.J., Davey, N.E., Van Roey, K., Altenberg, B., Toedt, G., Uyar, B., Seiler, M., Budd, A. et al. (2012) ELM-the database of eukaryotic linear motifs. Nucleic Acids Res., 40, D242-D251.
4. Guettler, S., Larose, J., Petsalaki, E., Gish, G., Scotter, A., Pawson, T., Rottapel, R. and Sicheri, F. (2011) Structural basis and sequence rules for substrate recognition by tankyrase explain the basis for cherubism disease. Cell, 147, 1340-1354.
5. Kadaveru, K., Vyas, J. and Schiller, M.R. (2008) Viral infection and human disease-insights from minimotifs. Front. Biosci., 13, 6455-6471.
6. Davey, N.E., Van Roey, K., Weatheritt, R.J., Toedt, G., Uyar, B., Altenberg, B., Budd, A., Diella, F., Dinkel, H. and Gibson, T.J. (2012) Attributes of short linear motifs. Mol. Biosyst., 8, 268-281.
7. Diella, F., Haslam, N., Chica, C., Budd, A., Michael, S., Brown, N.P., Trave, G. and Gibson, T.J. (2008) Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Front. Biosci., 13, 6580-6603.
8. Luck, K., Fournane, S., Kieffer, B., Masson, M., Nomine, Y. and Trave, G. (2011) Putting into practice domain-linear motif interaction predictions for exploration of protein networks. PLoS One, 6, e25376.
9. Rajasekaran, S., Balla, S., Gradie, P., Gryk, M.R., Kadaveru, K., Kundeti, V., Maciejewski, M.W., Mi, T., Rubino, N., Vyas, J. et al. (2009) Minimotif miner 2nd release: a database and web system for motif search. Nucleic Acids Res., 37, D185-D190.
10. Obenauer, J.C., Cantley, L.C. and Yaffe, M.B. (2003) Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res., 31, 3635-3641.
11. Chica, C., Labarga, A., Gould, C.M., Lopez, R. and Gibson, T.J. (2008) A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences. BMC Bioinformatics, 9, 229.
12. Davey, N.E., Haslam, N.J., Shields, D.C. and Edwards, R.J. (2011) SLiMSearch 2.0: biological context for short linear motifs in proteins. Nucleic Acids Res., 39, W56-W60.
13. Dinkel, H. and Sticht, H. (2007) A computational strategy for the prediction of functional linear peptide motifs in proteins. Bioinformatics, 23, 3297-3303.
14. Dosztanyi, Z., Csizmok, V., Tompa, P. and Simon, I. (2005) IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics, 21, 3433-3434.
15. Meszaros, B., Simon, I. and Dosztanyi, Z. (2009) Prediction of protein-binding regions in disordered proteins. PLoS Comput. Biol., 5, e1000376.
16. Via, A., Gould, C.M., Gemund, C., Gibson, T.J. and Helmer-Citterich, M. (2009) A structure filter for the eukaryotic linear motif resource. BMC Bioinformatics, 10, 351.
17. Petsalaki, E., Stark, A., Garcia-Urdiales, E. and Russell, R.B. (2009) Accurate prediction of peptide-binding sites on protein surfaces. PLoS Comput. Biol., 5, e1000335.
18. Ramu, C. (2003) SIRW: a web server for the simple indexing and retrieval system that combines sequence motif searches with keyword searches. Nucleic Acids Res., 31, 3771-3774.
19. Edwards, R.J., Davey, N.E. and Shields, D.C. (2007) SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins. PLoS One, 2, e967.
20. Lieber, D.S., Elemento, O. and Tavazoie, S. (2010) Large-scale discovery and characterization of protein regulatory motifs in eukaryotes. PLoS One, 5, e14444.
21. Neduva, V., Linding, R., Su-Angrand, I., Stark, A., de Masi, F., Gibson, T.J., Lewis, J., Serrano, L. and Russell, R.B. (2005) Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol., 3, e405.
22. Xue, B., Dunker, A.K. and Uversky, V.N. (2010) Retro-MoRFs: identifying protein binding sites by normal and reverse alignment and intrinsic disorder prediction. Int. J. Mol. Sci., 11, 3725-3747.
23. Encinar, J.A., Fernandez-Ballester, G., Sanchez, I.E., Hurtado-Gomez, E., Stricher, F., Beltrao, P. and Serrano, L. (2009) ADAN: a database for prediction of protein-protein interaction of modular domains mediated by linear motifs. Bioinformatics, 25, 2418-2424.
24. Linding, R., Jensen, L.J., Pasculescu, A., Olhovsky, M., Colwill, K., Bork, P., Yaffe, M.B. and Pawson, T. (2008) NetworKIN: a resource for exploring cellular phosphorylation networks. Nucleic Acids Res., 36, D695-D699.
25. Fuxreiter, M., Tompa, P. and Simon, I. (2007) Local structural disorder imparts plasticity on linear motifs. Bioinformatics, 23, 950-956.
26. Eddy, S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
27. Stein, A., Ceol, A. and Aloy, P. (2011) 3Did: identification and classification of domain-based interactions of known three-dimensional structure. Nucleic Acids Res., 39, D718-D723.
28. Finn, R.D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J.E., Gavin, O.L., Gunasekaran, P., Ceric, G., Forslund, K. et al. (2010) The pfam protein families database. Nucleic Acids Res., 38, D211-D222.
29. UniProt Consortium. (2010) The universal protein resource (UniProt) in 2010. Nucleic Acids Res., 38, D142-D148.
30. Davey, N.E., Edwards, R.J. and Shields, D.C. (2007) The SLiMDisc server: short, linear motif discovery in proteins. Nucleic Acids Res., 35, W455-W459.
31. Flicek, P., Amode, M.R., Barrell, D., Beal, K., Brent, S., Chen, Y., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S. et al. (2011) Ensembl 2011. Nucleic Acids Res., 39, D800-D806.
32. Szklarczyk, D., Franceschini, A., Kuhn, M., Simonovic, M., Roth, A., Minguez, P., Doerks, T., Stark, M., Muller, J., Bork, P. et al. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res., 39, D561-D568.
33. Dinkel, H., Chica, C., Via, A., Gould, C.M., Jensen, L.J., Gibson, T.J. and Diella, F. (2011) Phospho.ELM: a database of phosphorylation sites-update 2011. Nucleic Acids Res., 39, D261-D267.