Using neighborhood cohesiveness to infer interactions between protein domains

Bioinformatics

Volumn 31, Issue 15, 2015, Pages 2545-2552

  Segura, Joan ^a   Sorzano, C O S ^a   Cuenca Alba, Jesus ^a   Aloy, Patrick ^b,c   Carazo, J M ^a  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

^b INSTITUTE FOR RESEARCH IN BIOMEDICINE   (Spain)

^c INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ALGORITHM; BIOLOGY; CHEMISTRY; CLUSTER ANALYSIS; GENE EXPRESSION REGULATION; HUMAN; METABOLISM; PROCEDURES; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN PROTEIN INTERACTION; PROTEIN TERTIARY STRUCTURE;

ALGORITHMS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; GENE EXPRESSION REGULATION; HUMANS; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 84943628491     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv188     Document Type: Article

References (44)

1. Apic, G. et al. (2001) Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J. Mol. Biol., 310, 311-325.
2. Ben-Hur, A. and Noble, W. S. (2006) Choosing negative examples for the prediction of protein-protein interactions. BMC bioinformatics, 7(Suppl. 1), S2.
3. Berggard, T. et al. (2007) Methods for the detection and analysis of proteinprotein interactions. Proteomics, 7, 2833-2842.
4. Blohm, P. et al. (2014) Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis. Nucleic Acids Res., 42, D396-D400.
5. Chen, C. et al. (2011) Inferring domain-domain interactions using an extended parsimony model. In Systems Biology (ISB), 2011 IEEE International Conference on IEEE, pp. 374-378.
6. Deng, M. et al. (2002) Inferring domain-domain interactions from protein-protein interactions. Genome Res., 12, 1540-1548.
7. Desjarlais, J. R. and Berg, J. M. (1992) Toward rules relating zinc finger protein sequences and DNA binding site preferences. Proc. Natl. Acad. Sci. U. S. A., 89, 7345-7349.
8. Ekman, D. et al. (2005) Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions. J. Mol. Biol., 348, 231-243.
9. Finn, R. D. et al. (2014) Pfam: the protein families database. Nucleic Acids Res., 42, D222-D230.
10. Franceschini, A. et al. (2013) STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res., 41, D808-D815.
11. Goldberg, D. S. and Roth, F. P. (2003) Assessing experimentally derived interactions in a small world. Proc. Natl. Acad. Sci. U. S. A., 100, 4372-4376.
12. Gomez, S. M. et al. (2003) Learning to predict protein-protein interactions from protein sequences. Bioinformatics, 19, 1875-1881.
13. Gupta, S. et al. (2010) Unraveling the conundrum of seemingly discordant protein-protein interaction datasets. In: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society, pp. 783-786.
14. Halperin, I. et al. (2002) Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins, 47, 409-443.
15. Hamelryck, T. and Manderick, B. (2003) PDB file parser and structure class implemented in Python. Bioinformatics, 19, 2308-2310.
16. Hulovatyy, Y. et al. (2014) Revealing missing parts of the interactome via link prediction. PLoS One, 9, e90073.
17. Itzhaki, Z. et al. (2006) Evolutionary conservation of domain-domain interactions. Genome Biol., 7, R125.
18. Johnson, L. S. et al. (2010) Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinformatics, 11, 431.
19. Jothi, R. et al. (2006) Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating proteinprotein interactions. J. Mol. Biol., 362, 861-875.
20. Kanehisa, M. et al. (2014) Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res., 42, D199-D205.
21. Kann, M. G. et al. (2007) Predicting protein domain interactions from coevolution of conserved regions. Proteins, 67, 811-820.
22. Koh, H. et al. (2000) Inhibition of Akt and its anti-apoptotic activities by tumor necrosis factor-induced protein kinase C-related kinase 2 (PRK2) cleavage. J. Biol. Chem., 275, 34451-34458.
23. Li, S. et al. (2011) Network target for screening synergistic drug combinations with application to traditional Chinese medicine. BMC Syst. Biol., 5(Suppl. 1), S10.
24. Liu, M. et al. (2009) Knowledge-guided inference of domain-domain interactions from incomplete protein-protein interaction networks. Bioinformatics, 25, 2492-2499.
25. Liu, Y. et al. (2005) Inferring protein-protein interactions through highthroughput interaction data from diverse organisms. Bioinformatics, 21, 3279-3285.
26. Mosca, R. et al. (2012) The role of structural disorder in the rewiring of protein interactions through evolution. Mol. Cell. Proteomics, 11, M111 014969.
27. Mosca, R. et al. (2013) Interactome3D: adding structural details to protein networks. Nat. Methods, 10, 47-53.
28. Mosca, R. et al. (2014) 3did: a catalog of domain-based interactions of known three-dimensional structure. Nucleic Acids Res., 42, D374-D379.
29. Moya-Garcia, A. A. and Ranea, J. A. (2013) Insights into polypharmacology from drug-domain associations. Bioinformatics, 29, 1934-1937.
30. Ng, S. K. et al. (2003) Integrative approach for computationally inferring protein domain interactions. Bioinformatics, 19, 923-929.
31. Nye, T. M. et al. (2005) Statistical analysis of domains in interacting protein pairs. Bioinformatics, 21, 993-1001.
32. Palkowitsch, L. et al. (2008) Phosphorylation of serine 68 in the IkappaB kinase (IKK)-binding domain of NEMO interferes with the structure of the IKK complex and tumor necrosis factor-alpha-induced NF-kappaB activity. J. Biol. Chem., 283, 76-86.
33. Pawson, T. and Nash, P. (2003) Assembly of cell regulatory systems through protein interaction domains. Science, 300, 445-452.
34. Pazos, F. and Valencia, A. (2008) Protein co-evolution, co-adaptation and interactions. EMBO J., 27, 2648-2655.
35. Ravasz, E. et al. (2002) Hierarchical organization of modularity in metabolic networks. Science, 297, 1551-1555.
36. Riley, R. et al. (2005) Inferring protein domain interactions from databases of interacting proteins. Genome Biol., 6, R89.
37. Rose, P. W. et al. (2013) The RCSB protein data bank: new resources for research and education. Nucleic Acids Res., 41, D475-D482.
38. Segura, J. et al. (2011) Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi diagrams. BMC Bioinformatics, 12, 352.
39. Smoot, M. E. et al. (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics, 27, 431-432.
40. Sprinzak, E. and Margalit, H. (2001) Correlated sequence-signatures as markers of protein-protein interaction. J. Mol. Biol., 311, 681-692.
41. Watson, J. D. et al. (2005) Predicting protein function from sequence and structural data. Curr. Opin. Struct. Biol., 15, 275-284.
42. Watts, D. J. and Strogatz, S. H. (1998) Collective dynamics of 'small-world' networks. Nature, 393, 440-442.
43. Wu, Z. H. et al. (2006) Molecular linkage between the kinase ATM and NF-kappaB signaling in response to genotoxic stimuli. Science, 311, 1141-1146.
44. Yellaboina, S. et al. (2011) DOMINE: a comprehensive collection of known and predicted domain-domain interactions. Nucleic Acids Res., 39, D730-D735.