The birth, development and applications of domain-domain interaction databases

Progress in Biochemistry and Biophysics

Volumn 36, Issue 3, 2009, Pages 280-287

  Ouyang, Yu Mei ^a  

^a Yili Normal University   (China)

Author keywords

Database; Domain domain interactions (DDI); Protein domain; Protein protein interactions (PPI)

Indexed keywords

EID: 67650714288     PISSN: 10003282     EISSN: None     Source Type: Journal    
DOI: 10.3724/SP.J.1206.2008.00437     Document Type: Article

References (27)

1. Shoemaker B A, Panchenko A R. Deciphering protein-protein interactions. Part I . Experimental techniques and databases. PLoS Comput Biol, 2007, 3 (3): e42
2. Yu X Y, Xu Z P. Chin J Biochem Mol Biol, 2008, 24(3): 189-196
3. Shoemaker B A, Panchenko A R. Deciphering protein-protein interactions. Part Π . Computational methods to predict protein and domain interaction partners. PLoS Comput Biol, 2007, 3(4): e43
4. Deng M, Mehta S, Sun F, et al. Inferring domain-domain interactions from protein-protein interactions. Genome Res, 2002, 12(10): 1540-1548
5. Lee H, Deng M, Sun F, et al. An integrated approach to the prediction of domain-domain interactions. BMC Bioinfoπnatics, 2006, 7:269
6. Ng S K, Zhang Z, Tan S H. Integrative approach for computationally inferring protein domain interactions. Bioinfoπnatics, 2003, 19(8): 923-929
7. Pagel P, Wong P, Frishman D. A domain interaction map based on phylogenetic profiling. J Mol Biol, 2004, 344(5): 1331 -1346
8. Pagel P, Strack N, Oesterheld M, et al. Computational prediction of domain interactions. Methods Mol Biol, 2007, 396: 3̃15
9. Riley R, Lee C, Sabatti C, et al. Inferring protein domain interactions from databases of interacting proteins. Genome Biol, 2005, 6(10): R89
10. Chen X W, Liu M. Prediction of protein-protein interactions using random decision forest framework. Bioinformatics, 2005, 21(24): 4394-4400.
11. Guimaraes K S, Jothi R, Zotenko E, et al. Predicting domain-domain interactions using a parsimony approach. Genome Biol, 2006, 7(11):R104
12. Guimaraes K S, Przytycka T M. Interrogating domain-domain interactions with parsimony based approaches. BMC Bioinfoπnatics, 2008, 9: 171
13. Jothi R, Cherukuri P F, Tasneem A, et al. Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. J Mol Biol, 2006, 362(4): 861̃875
14. Iqbal M, Freitas A A, Johnson C G. Message-passing algorithms for the prediction of protein domain interactions from protein-protein interaction data. Bioinformatics, 2008, 24(18): 2064̃2070
15. Stein A, Russell R B, Aloy P. 3did: interacting protein domains of known three-dimensional structure. Nucl Acid Res, 2005, 33 (Database issue): D413̃D417
16. Finn R D, Marshall M, Bateman A. iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics, 2005, 21(3): 410-412
17. Ng S K, Zhang Z, Tan S H, et al. InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes. Nucl Acid Res, 2003, 31(1): 251-254
18. Pagel P, Oesterheld M, Tovstukhina O, et al. DIMA 2.0-predicted and known domain interactions. Nucl Acid Res, 2008, 36(Database issue): D651-D655
19. Raghavachari B, Tasneem A, Przytycka T M. DOMINE: a database of protein domain interactions. Nucl Acid Res, 2008, 36 (Database issue): D656-D661
20. Berman H, Henrick K, Nakamura H, et al. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucl Acid Res, 2007, 35(Database issue): D301- D303
21. Finn R D, Tate J, Mistry J, el al. The Pfam protein families database. Nucl Acid Res, 2008, 36(Database issue): D281-288
22. Mewes H W, Dietmann S, Frishman D, et al. MIPS: analysis and annotation of genome information in 2007. Nucl Acid Res, 2008, 36 (Database issue): D196̃201
23. Singhal M, Resat H. A domain-based approach to predict protein-protein interactions. BMC Bioinformatics, 2007, 8: 199
24. Kim I, Liu Y, Zhao H. Bayesian methods for predicting interacting protein pairs using domain information. Biometrics, 2007, 63 (3): 824̃833
25. Ramirez F, Schlicker A, Assenov Y, el al. Computational analysis of human protein interaction networks. Proteomics, 2007, 7(15): 2541 - 2552
26. Zhao X M, Wang Y, Chen L. Protein domain annotation with integration of heterogeneous information sources. Proteins, 2008, 2 (1):461̃473
27. Ng K L, Huang C H, Liu H C, et al. Applications of domain-domain interactions in pathway study. Comput Biol Chem, 2008, 32(2): 81̃87