- Research Article
- Open Access
Domain-Based Predictive Models for Protein-Protein Interaction Prediction
EURASIP Journal on Advances in Signal Processing volume 2006, Article number: 032767 (2006)
Protein interactions are of biological interest because they orchestrate a number of cellular processes such as metabolic pathways and immunological recognition. Recently, methods for predicting protein interactions using domain information are proposed and preliminary results have demonstrated their feasibility. In this paper, we develop two domain-based statistical models (neural networks and decision trees) for protein interaction predictions. Unlike most of the existing methods which consider only domain pairs (one domain from one protein) and assume that domain-domain interactions are independent of each other, the proposed methods are capable of exploring all possible interactions between domains and make predictions based on all the domains. Compared to maximum-likelihood estimation methods, our experimental results show that the proposed schemes can predict protein-protein interactions with higher specificity and sensitivity, while requiring less computation time. Furthermore, the decision tree-based model can be used to infer the interactions not only between two domains, but among multiple domains as well.
Fields S, Song O-K: A novel genetic system to detect protein-protein interactions. Nature 1989, 340(6230):245–246. 10.1038/340245a0
Ho Y, Gruhler A, Heilbut A, et al.: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 2002, 415(6868):180–183. 10.1038/415180a
Zhu H, Bilgin M, Bangham R, et al.: Global analysis of protein activities using proteome chips. Science 2001, 293(5537):2101–2105. 10.1126/science.1062191
Williams NE: Immunoprecipitation procedures. Methods in Cell Biology 2000, 62: 449–453.
Bollag DM: Gel-filtration chromatography. Methods in Molecular Biology 1994, 36: 1–9.
Hansen JC, Lebowitz J, Demeler B: Analytical ultracentrifugation of complex macromolecular systems. Biochemistry 1994, 33(45):13155–13163. 10.1021/bi00249a001
Doyle ML: Characterization of binding interactions by isothermal titration calorimetry. Current Opinion in Biotechnology 1997, 8(1):31–35. 10.1016/S0958-1669(97)80154-1
Lakey JH, Raggett EM: Measuring protein-protein interactions. Current Opinion in Structural Biology 1998, 8(1):119–123. 10.1016/S0959-440X(98)80019-5
Ito T, Tashiro K, Muta S, et al.: Toward a protein-protein interaction map of the budding yeast: a comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proceedings of the National Academy of Sciences of the United States of America 2000, 97(3):1143–1147. 10.1073/pnas.97.3.1143
Uetz P, Giot L, Cagney G, et al.: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403(6770):623–627. 10.1038/35001009
Kini RM, Evans JH: Prediction of potential protein-protein interaction sites from amino acid sequence. Identification of a fibrin polymerization site. FEBS Letters 1996, 385(1–2):81–86. 10.1016/0014-5793(96)00327-4
Jones S, Thornton JM: Prediction of protein-protein interaction sites using patch analysis. Journal of Molecular Biology 1997, 272(1):133–143. 10.1006/jmbi.1997.1233
Pazos F, Helmer-Citterich M, Ausiello G, Valencia A: Correlated mutations contain information about protein-protein interaction. Journal of Molecular Biology 1997, 271(4):511–523. 10.1006/jmbi.1997.1198
Dandekar T, Snel B, Huynen M, Bork P: Conservation of gene order: a fingerprint of proteins that physically interact. Trends in Biochemical Sciences 1998, 23(9):324–328. 10.1016/S0968-0004(98)01274-2
Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA: Protein interaction maps for complete genomes based on gene fusion events. Nature 1999, 402(6757):86–90. 10.1038/47056
Marcotte EM, Pellegrini M, Ng H-L, Rice DW, Yeates TO, Eisenberg D: Detecting protein function and protein-protein interactions from genome sequences. Science 1999, 285(5428):751–753. 10.1126/science.285.5428.751
Huynen M, Snel B, Lathe W III, Bork P: Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Research 2000, 10(8):1204–1210. 10.1101/gr.10.8.1204
Goh C-S, Bogan AA, Joachimiak M, Walther D, Cohen FE: Co-evolution of proteins with their interaction partners. Journal of Molecular Biology 2000, 299(2):283–293. 10.1006/jmbi.2000.3732
Pazos F, Valencia A: Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Engineering 2001, 14(9):609–614. 10.1093/protein/14.9.609
Lu L, Lu H, Skolnick J: MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins 2002, 49(3):350–364. 10.1002/prot.10222
Fariselli P, Pazos F, Valencia A, Casadia R: Prediction of protein-protein interaction sites in heterocomplexes with neural networks. European Journal of Biochemistry 2002, 269(5):1356–1361. 10.1046/j.1432-1033.2002.02767.x
Yan C, Honavar V, Dobbs D: Predicting protein-protein interaction sites from amino acid sequence. In Tech. Rep. ISU-CS-TR 02-11. Department of Computer Science at Iowa State University, Iowa State, Iowa, USA; 2002.
Zhou H-X, Shan Y: Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins 2001, 44(3):336–343. 10.1002/prot.1099
Bock JR, Gough DA: Predicting protein-protein interactions from primary structure. Bioinformatics 2001, 17(5):455–460. 10.1093/bioinformatics/17.5.455
Jansen R, Haiyuan Y, Greenbaum D, et al.: A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 2003, 302(5644):449–453. 10.1126/science.1087361
Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D: A combined algorithm for genome-wide prediction of protein function. Nature 1999, 402(6757):83–86. 10.1038/47048
Martin S, Roe D, Faulon J-L: Predicting protein-protein interactions using signature products. Bioinformatics 2005, 21(2):218–226. 10.1093/bioinformatics/bth483
Deng M, Mehta S, Sun F, Chen T: Inferring domain-domain interactions from protein-protein interactions. Genome Research 2002, 12(10):1540–1548. 10.1101/gr.153002
Han DS, Kim HS, Seo J, Jang WH: A domain combination based probabilistic framework for protein-protein interaction prediction. Genome Informatics 2003, 14: 250–259.
Han DS, Kim HS, Jang WH, Lee SD, Suh JK: PreSPI: design and implementation of protein-protein interaction prediction service system. Genome Informatics 2004, 15(2):171–180.
Huang C, Kanaan SP, Wuchty S, Chen DZ, Izaguirre JA: Predicting protein-protein interactions from protein domains using a set cover approach. to appear in IEEE/ACM Transactions on Computational Biology and Bioinformatics
Kim WK, Park J, Suh JK: Large scale statistical prediction of protein-protein interaction by potentially interacting domain (PID) pair. Genome Informatics 2002, 13: 42–50.
Rain J-C, Selig L, De Reuse H, et al.: The protein-protein interaction map of Helicobacter pylori. Nature 2001, 409(6817):211–215. 10.1038/35051615
Ng SK, Zhang Z, Tan SH, Lin K: InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes. Nucleic Acids Research 2003, 31(1):251–254. 10.1093/nar/gkg079
Wojcik J, Schachter V: Protein-protein interaction map inference using interacting domain profile pairs. Bioinformatics 2001, 17(suppl. 1):S296–S305.
Ng SK, Zhang Z, Tan SH: Integrative approach for computationally inferring protein domain interactions. Bioinformatics 2003, 19(8):923–929. 10.1093/bioinformatics/btg118
Quinlan JR: Discovering rules from large collections of examples: a case study. In Expert Systems in the Micro Electronic Age. Edited by: Michie D. Edinburgh University of Press, Edinburgh, Scotland; 1979.
Xenarios I, Fernandez E, Salwinski L, et al.: DIP: The Database of Interacting Proteins. https://doi.org/dip.doe-mbi.ucla.edu
Schwikowski B, Uetz P, Fields S: A network of protein-protein interactions in yeast. Nature Biotechnology 2000, 18(12):1257–1261. 10.1038/82360
Bateman A, Coin L, Durbin R, et al.: The Pfam protein families database. Nucleic Acids Research 2004, 32(suppl. 1):D138–D141.
About this article
Cite this article
Chen, XW., Liu, M. Domain-Based Predictive Models for Protein-Protein Interaction Prediction. EURASIP J. Adv. Signal Process. 2006, 032767 (2006). https://doi.org/10.1155/ASP/2006/32767
- Neural Network
- Decision Tree
- Protein Interaction
- Predictive Model
- Quantum Information