Các phương pháp tính toán trong việc dự đoán các tương tác giữa protein: Một khảo sát

Walhout AJM, Vidal M (2001) Protein interactions maps for model organisms. Nat Rev Mol Cell Biol 2:55–62 Alberts B (1998) The cell as a collection of protein machines: Preparing the next generation of molecular biologists. Cell 92:291–294 Semple JI, Sanderson CM, Campbell RD (2002) The jury is out on “guilt by association” trials. Brief Funct Genomics Proteomics 1(1):40–52 von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P (2002) Comparative assessment of large-scale data sets of protein–protein interactions. Nature 417(6887):399–403 Deane CM, Salwinski L, Xenarios I, Eisenberg D. (2002) Protein interactions: Two methods for assessment of the reliability of high throughput observations. Mol and Cell Proteomics 1:349–356 Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 98(8):4569–4574 Mrowka R, Patzak A, Herzel H (2001) Is there a bias in proteome research? Genome Res 11(12):1971–1973 Edwardsm AM, Kus B, Jansen R, Greenbaum D, Greenblatt J, Gerstein M (2002) Bridging structural biology and genomics: Assessing protein interaction data with known complexes. Trends Genet 18(10):529–536 Fields S, Song O-K (1989) A novel genetic system to detect protein–protein interactions. Nature 340(6230):245–246 Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, et al. (2000) A comprehensive analysis of protein–protein interactions in Saccharomyces Cerevisiae. Nature 403(6770):623–627 Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JD, Chesneau A, Hao T, et al. (2004) A map of the interactome network of the metazoan C Elegans Science 303(5657):540–543 Giot L, et al. (2003) A protein interaction map of Drosophila melanogaster. Science 302:1727–1736 Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams S-L, Millar A, Taylor P, Bennett K, Boutilier K, et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415(6868):180–183 Gavin A-C, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon A-M, Cruciat C-M, et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415(6868):141–147 Bader GD, Hogue CWV (2002) Analyzing yeast protein–protein interaction data obtained from different sources. Nat Biotechnol 20(10):991–997 Valencia A, Pazos F (2002) Computational methods for the prediction of protein interactions. Curr Opin Struct Biol 12:368–373 Dandekar T, Snel B, Huynen M, Bork P (1998) Conservation of gene order: A fingerprint of proteins that physically interact. Science 23:324–328 Marcotte EM, Pellegrini M, Ng H-L, Rice DW, Yeates TO, Eisenberg D (1999) Detecting protein function and protein–protein interactions from genome sequences. Science 285:751–753 Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA (1999) Protein interactions maps for complete genomes based on gene fusion events. Nature 402(6747):86–90 Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO (1999) Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc Natl Acad Sci USA 96(8):4285–4288 Eisenberg D, Marcotte EM, Xenarios I, Yeates TO (2000) Protein function in the post-genomic era. Nature 405(6788):823–826 Schachter V (2002) Bioinformatics of large-scale protein interaction networks. BioTech Comput Proteomics Suppl 32:S16–S27 von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B (2003) STRING: a database of predicted functional associations between proteins. Nucl Acids Res 13(1):258–261 Bowers PM, Pellegrini M, Thompson MJ, Fierro J, Yeates TO, Eisenberg D (2004) Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol 5(5):R35 Mellor JC, Yanai I, Clodfelter KH, Mintseris J, DeLisi C (2002) Predictome: A database of putative functional links between proteins. Nucl Acids Res 30(1):306–309 Pazos F, Valencia A (2001) Similarity of phylogenetic trees as indicator of protein–protein interaction. Protein Eng 14(9):609–614 Gertz J, Elfond G, Shustrova A, Weisinger M, Pellegrini M, Cokus S, Rothschild B (2003) Inferring protein interactions from phylogenetic distance matrices. Bioinformatics 19(16):2039–2045 Matthews LR, Vaglio P, Reboul J, Ge H, Davis BP, Garrels J, Vincent S, Vidal M (2001) Identification of potential interaction networks using sequence-based searches for conserved protein–protein interactions or “interologs”. Genome Res 11(12):2120–2126 Wojcik J, Schachter V (2001) Protein–protein interaction map inference using interaction domain profile pairs. Bioinformatics 17(Suppl. 1):S296–S305 Bock JR, Gough DA (2003) Whole-proteome interaction mining. Bioinformatics 19(1):125–134 Gomez SM, Rzhetsky A (2002) Towards the prediction of complete protein–protein interaction networks. Pac Symp Biocomput 413–424 Deng M, Metha S, Sun F, Chen T (2002) Inferring domain–domain interactions from protein–protein interactions. In Proceedings of the 6th ACM International Conference on Research in Computational Molecular Biology (RECOMB), Washington, DC, USA Sprinzak E, Margalit H (2001) Correlated sequence-signatures as markers of protein–protein interaction. J Mol Biol 311(4):681–692 Kanaan SP, Huang C, Wuchty S, Chen D, Izaguirre JA (2005) Inferring protein–protein interactions from protein domain combinations. In Proceedings of the Ninth Annual International Conference on Research in Computational Molecular Biology Lu L, Lu H, Skolnick J (2002) MULTIPROSPECTOR: an algorithm for the prediction of protein–protein interactions by multimeric threading. Proteins Struct Funct Genet 49(3):350–364 Bock JR, Gough DA (2001) Predicting protein–protein interactions from primary structure. Bioinformatics 17(5):455–460 Jansen R, Lan N, Qian J, Gerstein M (2002) Integration of genomic datasets to predict protein complexes in yeast. J Struct Funct Genomics 2(2):71–81 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 Zhang LV, Wong SL, King OD, Roth FP (2004) Predicting co-complexed protein pairs using genomic and proteomic data integration. BMC Bioinformatics 5(38) Weiss GM (1995) Learning with rare cases and small disjuncts. In Proceedings of the 12th International Conference on Machine Learning, pp. 558–565 Stanyon CA, Liu G, Mangiola BA, Patel N, Giot L, Kuang B, Zhang H, Zhong J, Finley RL, Jr. (2004) A Drosophila protein-interaction map centered on cell-cycle regulators. Genome Biol 5(12):R96 Grigoriev A (2003) On the number of protein–protein interactions in the yeast proteome. Nucl Acids Res 31(14):4157–4161 Legrain P, Wojcik J, Gauthier J-M (2001) Protein–protein interaction maps: A lead towards cellular functions. Trends Genet 17(6):346–352 Tucker CL, Gera JF, Uetz P (2001) Towards an understanding of complex protein networks. Trends Cell Biol 11(3):102–106 Sprinzak E, Sattath S, Margalit H (2003) How reliable are experimental protein–protein interaction data? J Mol Biol 327(5):919–923 Walhout AJM, Boulton SJ, Vidal M (2000) Yeast two-hybrid systems and protein interaction mapping projects for yeast and worm. Yeast 17:88–94