Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method

Molecular Systems Biology

Volumn 4, Issue , 2008, Pages

  Burger, Lukas ^a   Van Nimwegen, Erik ^a  

^a UNIVERSITY OF BASEL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

PHOSPHOTRANSFERASE; POLYKETIDE SYNTHASE; REGULATOR PROTEIN; BACTERIAL PROTEIN;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; BAYES THEOREM; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; ALGORITHM; BACTERIUM; BINDING SITE; BIOLOGICAL MODEL; BIOLOGY; CAULOBACTER CRESCENTUS; CHEMICAL STRUCTURE; CHEMISTRY; ENZYMOLOGY; GENETICS; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; MONTE CARLO METHOD; PHOSPHORYLATION; PHYLOGENY; PREDICTION AND FORECASTING; PROBABILITY; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN TERTIARY STRUCTURE; QUALITY CONTROL; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT;

BACTERIA (MICROORGANISMS);

ALGORITHMS; AMINO ACID SEQUENCE; BACTERIA; BACTERIAL PROTEINS; BAYES THEOREM; BENCHMARKING; BINDING SITES; CAULOBACTER CRESCENTUS; COMPUTATIONAL BIOLOGY; GENOME, BACTERIAL; MARKOV CHAINS; MODELS, BIOLOGICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MONTE CARLO METHOD; PHOSPHORYLATION; PHYLOGENY; POLYKETIDE SYNTHASES; PREDICTIVE VALUE OF TESTS; PROBABILITY; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, TERTIARY; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SIGNAL TRANSDUCTION;

EID: 39149114704     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb4100203     Document Type: Article

References (27)

1. Alm E, Huang K, Arkin A (2006) The evolution of two-component systems in bacteria reveals different strategies for niche adaptation. PLoS Comp Biol 2: e143
2. Ausmees N, Jacobs-Wagner C (2003) Spatial and temporal control of differentiation and cell cycle progression in Caulobacter crescentus. Annu Rev Microbiol 57: 225-247
3. Bateman A, Coin L, Durbin R, Finn R, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer E, Studholme D, Yeats C, Eddy S (2004) The Pfam protein families database. Nucleic Acids Res 32: D138-D141
4. Biondi E, Reisinger S, Skerker J, Arif M, Perchuk B, Ryan K, Laub M (2006) Regulation of the bacterial cell cycle by an integrated genetic circuit. Nature 444: 899-904
5. Bork P, Jensen L, von Mering C, Ramani A, Lee I, Marcotte E (2004) Protein interaction networks from yeast to human. Curr Opin Struct Biol 14: 292-299
6. Cerquides J, de Màntaras RL (2003) Tractable Bayesian learning of tree augmented naive Bayes classifiers. Proceedings of Twentieth International Conference on Machine Learning. Menlo Park, California: AAAI Press
7. Fabret C, Feher V, Hoch J (1999) Two-component signal transduction in Bacillus subtilis: how one organism sees its world. J Bacteriol 181: 1975-1983
8. Grebe T, Stock J (1999) The histidine protein kinase superfamily. Adv Microb Physiol 41: 139-227
9. Higgins CF (1992) ABC transporters: from microorganisms to man. Annu Rev Cell Biol 8: 67-113
10. Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M (2003) A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302: 449-453
11. Jaynes ET (2003) Probability Theory: the Logic of Science. Cambridge, UK: Cambridge University Press
12. Kaczmarski R, Mufti GJ (1991) The cytokine receptor superfamily. Blood Rev 5: 193-203
13. Koretke K, Lupas A, Warren P, Rosenberg M, Brown J (2000) Evolution of two-component signal transduction. Mol Biol Evol 17: 1956-1968
14. Lockless SW, Ranganathan R (1999) Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286: 295-299
15. Meilá M, Jaakkola T (2006) Tractable Bayesian learning of tree belief networks. Statistics Computing 16: 77-92
16. Ohta N, Newton A (2003) The core dimerization domains of histidine kinases contain specificity for the cognate response regulator. J Bacteriol 185: 4424-4431
17. Pazos F, Valencia A (2002) In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins 47: 219-227
18. Shoemaker BA, Panchenko AR (2007) Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners. PLoS Comput Biol 3: e43
19. Skerker J, Laub M (2004) Cell-cycle progression and the generation of asymmetry in Caulobacter crescentus. Nat Rev Microbiol 3: 325-337
20. Skerker J, Prasol M, Perchuk B, Biondi E, Laub M (2005) Two-component signal transduction pathways regulating growth and cell cycle progression in a bacterium: a systems-level analysis. PLoS Biol 3: e334
21. Stock A, Robinson V, Goudreau P (2000) Two-component signal transduction. Annu Rev Biochem 69: 183-215
22. Thattai M, Burak Y, Shraiman BI (2007) The origins of specificity in polyketide synthase protein interactions. PLoS Comp Biol 3: e186
23. Valencia A, Pazos F (2002) Computational methods for the prediction of protein interactions. Curr Opin Struct Biol 12: 368-373
24. van Nimwegen E (2003) Scaling laws in the functional content of genomes. Trends Genet 19: 479-484
25. Weissman K, Leadlay P (2005) Combinatorial biosynthesis of reduced polyketides. Nat Rev Microbiol 3: 925-936
26. Wu J, Ohta JL, Newton A (1999) A novel bacterial tyrosine kinase essential for cell division and differentiation. Proc Natl Acad Sci USA 96: 13068-13073
27. Zapf J, Sen U, Madhusudan M, Hoch JA, Varughese KI (2000) A transient interaction between two phosphorelay proteins trapped in a crystal lattice reveals the mechanism of molecular recognition and phosphotransfer in signal transduction. Structure 8: 851-862