Protein fold recognition by functional domain composition

Progress in Biochemistry and Biophysics

Volumn 38, Issue 2, 2011, Pages 166-172

  Yan, Jin Li ^a   Chen, Zhi Wei ^a   Xu, Hai Song ^a   Li, Xiao Qin ^a  

^a BEIJING UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

Fold recognition; Fold type; Functional domain; LIFCA

Indexed keywords

EID: 79951876780     PISSN: 10003282     EISSN: None     Source Type: Journal    
DOI: 10.3724/SP.J.1206.2010.00345     Document Type: Article

References (28)

1. Burley S K. An overview of structural genomics. Nature Structural Biology, 2000, 7(Suppl.): 932-934
2. Baker D, Sali A. Protein structure prediction and structural genomics. Science, 2001, 294(5): 93-96 (Pubitemid 32952955)
3. Murzin A G, Brenner S E, Hubbard T, et al. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Molecular Biology, 1995, 247(4): 536-540
4. Lo Conte L, Brenner S E, Hubbard T, et al. SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Research, 2002, 30(1): 264-267 (Pubitemid 34679560)
5. Orengo C A, Michie A D, Jones S, et al. CATH: A hierarchic classification of protein domain structures. Structure, 1997, 5 (8): 1093-1108 (Pubitemid 27393093)
6. Pearl F, Todd A, Sillitoe I, et al. The CATH domain structure database and related resources Gene3D and DHS providecomprehensive domain family information for genome analysis. Nucleic Acids Research, 2005, 33(1): D247-D251 (Pubitemid 40207871)
7. Novotny M, Madsen D, Kleywegt G J. Evaluation of protein fold comparison servers. Proteins, 2004, 54(2): 260-270 (Pubitemid 38084067)
8. Matsuda K, Nishioka T, Kinoshita K. Finding evolutionary relations beyond superfamilies: Fold-based superfamilies. Protein Science, 2003, 12 (10): 2239-2251 (Pubitemid 37163357)
9. Chen Y, Crippen G M. Fold recognition via a tree. J Computational Biology, 2006, 13(9): 1565-1573 (Pubitemid 44888229)
10. Dubchak I, Muchnik I, Holbrook S R, et al. Prediction of protein folding class using global description of amino acid sequence. Proc Natl Acad Sci USA, 1995, 92(19): 8700-8704
11. Dubchak I, Muchnik I, Mayor C, et al. Recognition of a protein fold in the context of the SCOP classification. Proteins: Structure, Function and Genetics, 1999, 35(4): 401-407 (Pubitemid 29264836)
12. Ding C H, Dubchak I. Multi-class protein fold recognition using support vector machines and neural networks. Bioinformatics, 2001, 17(4): 349-358 (Pubitemid 32421929)
13. Shi J Y, Pan Q, Zhang S W, et al. Prog Biochem Biophys, 2006, 33(2): 155-162
14. Jain P, Garibaldi J M, Hirst J D. Supervised machine learning algorithms for protein structure classification. Computational Biology and Chemistry. 2009, 33(3): 216-223
15. Marsolo K, Parthasarathy S, Ding C. A multi-level approach to SCOP fold recognition. Proceedings of the Fifth IEEE Symposium on Bioinformatics and Bioengineering. Washington, DC: IEEE Computer Society, 2005: 57-64 (Pubitemid 44773489)
16. Marsolo K, Parthasarathy S. Alternate representation of distance matrices for characterization of protein structure. Proceedings of the Fifth IEEE International Conference on Data Mining. Washington, DC: IEEE Computer Society, 2005: 298-305 (Pubitemid 47385706)
17. Shi J Y, ZhangYN. Acta Biophysica sinica, 2009, 25(2): 106-116
18. Shen HB, Chou KC. Predicting protein fold pattern with functional domain and sequential evolution information. J Theoretical Biology, 2009, 256(3): 441-446
19. Gewehr J E, Hintermair V, Zimmer R. AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings. Bioinformatics, 2007, 23(10): 1203-1210 (Pubitemid 47050535)
20. Luo L F, Li X Q. Recognition and architecture of the framework structure of protein. Proteins, 2000, 39(1): 9
21. Liu X H, Li X Q, Xu H S, et al. Chin J Biochem Mol Biol, 2008, 24(8): 761
22. Zhang W, Li X Q, Xu H S, et al. Acta Biophysica Sinica, 2008, 24(1): 65
23. Ren W K, Xu H S, Li X Q. Prog Biochem Biophys, 2007, 35(5): 548-554
24. Liu Y, Li X Q, Xu H S, et al. Acta Physico-Chimica Sinica, 2009, 25(12): 2558-2564
25. Chou K C, Cai Y D. Predicting subcellular localization of proteins by hybridizing functional domain composition and pseudo-amino acid composition. J Cell Biochem, 2004, 91(6): 1197-1203
26. Xu X C, Yu D, Fang W, et al. Prediction of peptidase category based on functional domain composition. J Proteome Research, 2008, 7(10): 4521-4524
27. ChouK C, Cai YD. Predicting protein structural class by functional domain composition. Biochem Biophys Res Commun, 2004, 321(4): 1007-1009
28. Finn R D, Mistry J, Schuster-Bockler B, et al. Pfam: clans, web tools and services. Nucleic Acids Res, 2006, 34(1): D247-D25