PepSite: Prediction of peptide-binding sites from protein surfaces

Nucleic Acids Research

Volumn 40, Issue W1, 2012, Pages

  Trabuco, Leonardo G ^a   Lise, Stefano ^b   Petsalaki, Evangelia ^c,d   Russell, Robert B ^a  

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c MOUNT SINAI HOSPITAL   (Canada)

^d UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING SITE; CALCULATION; COMPUTER PROGRAM; INTERNET; PREDICTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SURFACE PROPERTY; THREE DIMENSIONAL IMAGING; WEB SERVER;

BINDING SITES; INTERNET; PEPTIDES; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN INTERACTION MAPPING; PROTEINS; SOFTWARE;

EID: 84864419151     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks398     Document Type: Article

References (41)

1. 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.
2. Diella, F., Haslam, N., Chica, C., Budd, A., Michael, S., Brown, N.P., Traveg. and Gibson, T.J. (2008) Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Front. Biosci., 13, 6580-6603.
3. Wen, W., Meinkotht, J.L., Tsien, R.Y. and Taylor, S.S. (1995) Identification of a signal for rapid export of proteins from the nucleus. Cell, 82, 463-473.
4. Boll, W., Rapoport, I., Brunner, C., Modis, Y., Prehn, S. and Kirchhausen, T. (2002) The m2 subunit of the clathrin adaptor AP-2 binds to FDNPVY and Yppsorting signals at distinct sites. Traffic, 3, 590-600.
5. Miller, M.L., Jensen, L.J., Diella, F., Jgensen, C., Tinti, M., Li, L., Hsiung, M., Parker, S.A., Bordeaux, J., Sicheritz-Ponten, T. et al. (2008) Linear motif atlas for phosphorylation-dependent signaling. Sci. Signal., 1, ra2.
6. Scott, J.D. and Pawson, T. (2009) Cell signaling in space and time: where proteins come together and when they're apart. Science, 326, 1220-1224.
7. 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.
8. Maclaine, N.J. and Hupp, T.R. (2011) How phosphorylation controls p53. Cell Cycle, 10, 916-921.
9. Soni, V., Cahir-McFarland, E. and Kieff, E. (2007) LMP1 TRAFficking activates growth and survival pathways. Adv. Exp. Med. Biol., 597, 173-187.
10. Dahiya, A., Gavin, M.R., Luo, R.X. and Dean, D.C. (2000) Role of the LXCXE binding site in Rb function. Mol. Cell Biol., 20, 6799-6805.
11. Vassilev, L.T., Vu, B.T., Graves, B., Carvajal, D., Podlaski, F., Filipovic, Z., Kong, N., Kammlott, U., Lukacs, C., Klein, C. et al. (2004) In vivo activation of the p53 pathway by small-molecule antagonists of MDM2. Science, 303, 844-848.
12. Yang, Y., Ludwig, R.L., Jensen, J.P., Pierre, S.A., Medaglia, M.V., Davydov, I.V., Safiran, Y.J., Oberoi, P., Kenten, J.H., Phillips, A.C. et al. (2005) Small molecule inhibitors of HDM2 ubiquitin ligase activity stabilize and activate p53 in cells. Cancer Cell, 7, 547-559.
13. Kadaveru, K., Vyas, J. and Schiller, M.R. (2008) Viral infection and human disease-insights from minimotifs. Front. Biosci., 13, 6455-6471.
14. 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.
15. 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.
16. Sigrist, C.J.A., Cerutti, L., de Castro, E., Langendijk-Genevaux, P.S., Bulliard, V., Bairoch, A. and Hulo, N. (2010) PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res., 38, D161-D166.
17. 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.
18. Encinar, J.A., Fernandez-Ballester, G., Sánchez, 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.
19. Mooney, C., Pollastri, G., Shields, D.C. and Haslam, N.J. (2012) Prediction of short linear protein binding regions. J. Mol. Biol., 415, 193-204.
20. Davey, N.E., Edwards, R.J. and Shields, D.C. (2010) Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins. BMC Bioinformatics, 11, 14.
21. Neduva, V. and Russell, R.B. (2006) DILIMOT: discovery of linear motifs in proteins. Nucleic Acids Res., 34, W350-W355.
22. Jonassen, I., Collins, J.F. and Higgins, D.G. (1995) Finding flexible patterns in unaligned protein sequences. Protein Sci., 4, 1587-1595.
23. 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.
24. Heteyi, C. and van der Spoel, D. (2002) Efficient docking of peptides to proteins without prior knowledge of the binding site. Protein Sci., 11, 1729-1737.
25. Tong, A.H.Y., Drees, B., Nardelli, G., Bader, G.D., Brannetti, B., Castagnoli, L., Evangelista, M., Ferracuti, S., Nelson, B., Paoluzi, S. et al. (2002) A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science, 295, 321-324.
26. Dalby, P.A., Hoess, R.H. and DeGrado, W.F. (2000) Evolution of binding affinity in a WW domain probed by phage display. Protein Sci., 9, 2366-2376.
27. Wiedemann, U., Boisguerin, P., Leben, R., Leitner, D., Krause, G., Moelling, K., Volkmer-Engert, R. and Oschkinat, H. (2004) Quantification of PDZ domain specificity, prediction of ligand affinity and rational design of super-binding peptides. J. Mol. Biol., 343, 703-718.
28. Ghersi, D. and Sanchez, R. (2011) Beyond structural genomics: computational approaches for the identification of ligand binding sites in protein structures. J. Struct. Funct. Genomics, 12, 109-117.
29. Capra, J.A. and Singh, M. (2007) Predicting functionally important residues from sequence conservation. Bioinformatics, 23, 1875-1882.
30. Hernandez, M., Ghersi, D. and Sanchez, R. (2009) SITEHOUNDweb: a server for ligand binding site identification in protein structures. Nucleic Acids Res., 37, W413-W416.
31. Petsalaki, E., Stark, A., Garcí-Urdiales, E. and Russell, R.B. (2009) Accurate prediction of peptide binding sites on protein surfaces. PLoS Comput. Biol., 5, e1000335.
32. London, N., Raveh, B., Cohen, E., Fathi, G. and Schueler-Furman, O. (2011) Rosetta FlexPepDock web server-high resolution modeling of peptide-protein interactions. Nucleic Acids Res., 39, W249-W253.
33. Raveh, B., London, N., Zimmerman, L. and Schueler-Furman, O. (2011) Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors. PLoS ONE, 6, e18934.
34. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000) The protein data bank. Nucleic Acids Res., 28, 235-242.
35. Stark, A. and Russell, R.B. (2003) Annotation in three dimensions. PINTS: patterns in non-homologous tertiary structures. Nucleic Acids Res., 31, 3341-3344.
36. Russell, R.B. and Barton, G.J. (1992) Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins, 14, 309-323.
37. Humphrey, W., Dalke, A. and Schulten, K. (1996) VMD: visual molecular dynamics. J. Mol. Graph, 14, 33-38.
38. Murai, M.J., Chruszcz, M., Reddy, G., Grembecka, J. and Cierpicki, T. (2011) Crystal structure of menin reveals binding site for mixed lineage leukemia (MLL) protein. J. Biol. Chem., 286, 31742-31748.
39. Yokoyama, A., Somervaille, T.C.P., Smith, K.S., Rozenblatt-Rosen, O., Meyerson, M. and Cleary, M.L. (2005) The menin tumor suppressor protein is an essential oncogenic cofactor for MLL-associated leukemogenesis. Cell, 123, 207-218.
40. Caslini, C., Yang, Z., El-Osta, M., Milne, T.A., Slany, R.K. and Hess, J.L. (2007) Interaction of MLL amino terminal sequences with menin is required for transformation. Cancer Res., 67, 7275-7283.
41. Grembecka, J., Belcher, A.M., Hartley, T. and Cierpicki, T. (2010) Molecular basis of the mixed lineage leukemia-menin interaction: implications for targeting mixed lineage leukemias. J. Biol. Chem., 285, 40690-40698.