A novel motif discovery algorithm for identifying protein families

Protein and Peptide Letters

Volumn 17, Issue 10, 2010, Pages 1215-1222

  Wei, Rong ^a   Gao, Lei ^b,c   Zhang, Tongliang ^d  

^a HEBEI POLYTECHNIC UNIVERSITY   (China)

^b UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^c DONGHUA UNIVERSITY   (China)

^d MOC   (China)

Author keywords

Ligases; Motif discovery; Prediction; Protein family; Protein motif; Sequence pattern matching

Indexed keywords

LIGASE; PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BIOLOGY; CLASSIFICATION; GENETICS; HUMAN; METHODOLOGY; MOLECULAR GENETICS; PROTEIN MOTIF;

ALGORITHMS; AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; COMPUTATIONAL BIOLOGY; HUMANS; LIGASES; MOLECULAR SEQUENCE DATA; PROTEINS;

EID: 77958483944     PISSN: 09298665     EISSN: None     Source Type: Journal    
DOI: 10.2174/092986610792231429     Document Type: Article

References (29)

1. Falquet, L.; Pagni, M.; Bucher, P.; Hulo, P.; Sigrist, C. J. A.; Hofmann, K.; Bairoch, A. The PROSITE database, its status in 2002. Nucleic Acids Res., 2002, 30(1), 235-238.
2. Hofmann, K.; Bucher, P.; Falquet, L.; Bairoch, A. The PROSITE database, its status in 1999. Nucleic Acids Res., 1999, 27(1), 215-219.
3. Chou, K. C.; Zheng, C. Strong electrostatic loop-helix interactions in bundle motif protein structures. Biophys. J., 1992, 63(3), 682-688.
4. Chou, K. C.; Maggiora, G. M.; Scheraga, H. A. Role of loop-helix interactions in stabilizing four-helix bundle proteins. Proc. Natl. Acad. Sci. U. S. A., 1992, 89(16), 7315.
5. Schnell, J. R.; Chou, J. J. Structure and mechanism of the M2 proton channel of influenza A virus. Nature, 2008, 451(7178), 591-595.
6. Tompa, M.; Li, N.; Bailey, T. L.; Church, G. M.; De Moor, B.; Eskin, E.; Favorov, A. V.; Frith, M. C.; Fu, Y.; Kent, W. J.; Makeev, V. J.; Mironov, A. A.; Noble, W. S.; Pavesi, G.; Pesole, G.; Régnier, M.; Simonis, N.; Sinha, S.; Thijs, G.; van Helden, J.; Vandenbogaert, M.; Weng, Z.; Workman, C.; Ye, C.; Zhu, Z. Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol., 2005, 23(1), 137-144.
7. Hu, J.; Li, B.; Kihara, D. Limitations and potentials of current motif discovery algorithms. Nucleic Acids Res., 2005, 33(15), 4899-4913.
8. Hon, A. S.; Jain, A. N. A deterministic motif finding algorithm with application to the human genome. Bioinformatics, 2006, 22(9), 1047-1054.
9. Liu, X. S.; Brutlag, D. L.; Liu, J. S. An algorithm for finding protein- DNA binding sites with applications to chromatinimmunoprecipitation microarray experiments. Nat. Biotechnol., 2002, 20(835-839).
10. Chou, K. C. Structural bioinformatics and its impact to biomedical science. Curr. Med. Chem., 2004, 11(16), 2105-2134.
11. Chang, B. C. H.; Halgamuge, S. K. Protein motif extraction with neuro-fuzzy optimization. Bioinformatics, 2002, 18(8), 1084-1090.
12. Hochbaum, D. S. Approximation algorithms for NP-hard problems. ACM SIGACT News, 1997, 28(2), 40-52.
13. Ben-Hur, A.; Brutlag, D. Remote homology detection: a motif based approach. Bioinformatics, 2003, 19(Suppl. 1), i26-i33.
14. Holm, L.; Sander, C. Removing near-neighbour redundancy from large protein sequence collections. Bioinformatics, 1998, 14(5), 423-429.
15. Shen, H. B.; Chou, K. C. EzyPred: a top-down approach for predicting enzyme functional classes and subclasses. Biochem. Biophys. Res. Commun., 2007, 364(1), 53-59.
16. Chou, K. C.; Jones, D.; Heinrikson, R. L. Prediction of the tertiary structure and substrate binding site of caspase-8. FEBS Lett., 1997, 419(1), 49-54.
17. Chou, K. C. Insights from modelling the 3D structure of the extracellular domain of alpha 7 nicotinic acetylcholine receptor. Biochem. Biophys. Res. Commun., 2004, 319(2), 433-438.
18. Chou, K. C. Modelling extracellular domains of GABA-A receptors: subtypes 1, 2, 3, and 5. Biochem. Biophys. Res. Commun., 2004, 316(3), 636-642.
19. Wei, D. Q.; Du, Q. S.; Sun, H.; Chou, K. C. Insights from modeling the 3D structure of H5N1 influenza virus neuraminidase and itsbinding interactions with ligands. Biochem. Biophys. Res. Commun., 2006, 344(3), 1048-1055.
20. Wang, J. F.; Wei, D. Q.; Lin, Y.; Wang, Y. H.; Du, H. L.; Li, Y. X.; Chou, K. C. Insights from modeling the 3D structure of NAD (P) H-dependent D-xylose reductase of Pichia stipitis and its binding interactions with NAD and NADP. Biochem. Biophys. Res. Commun., 2007, 359(2), 323-329.
21. Wang, S. Q.; Du, Q. S.; Chou, K. C. Study of drug resistance of chicken influenza A virus (H5N1) from homology-modeled 3D structures of neuraminidases. Biochem. Biophys. Res. Commun., 2007, 354 (3), 634-640.
22. Wei, D. Q.; Wang, J. F.; Chen, C.; Li, Y.; Chou, K. C. Molecular modeling of two CYP2C19 SNPs and its implications for personalized drug design. Prot. Pept. Letts., 2008, 15(1), 27-32.
23. Gao, L.; Ding, Y. S.; Dai, H.; Shao, S. H.; Huang, Z. D.; Chou, K. C. A novel fingerprint map for detecting SARS-CoV. J. Pharm. Biomed. Anal., 2006, 41(1), 246-250.
24. Chou, K. C.; Shen, H. B. Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms. Nat. Protoc., 2008, 3(2), 153-162.
25. Xiao, X.; Wang, P.; Chou, K. C. GPCR-CA: A Cellular Automaton Image Approach for Predicting G-Protein-Coupled Receptor Functional Classes. J. Comput. Chem., 2009, 311, 419.
26. Lin, W. Z.; Xiao, X.; Chou, K. C. GPCR-GIA: a web-server for identifying G-protein coupled receptors and their families with grey incidence analysis. Protein Eng. Des. Sel., 2009, 22(11), 699.
27. Chou, K.; Cai, Y. Prediction of protease types in a hybridization space. Biochem. Biophys. Res. Commun., 2006, 339(3), 1015-1020.
28. Chou, K. C.; Shen, H. B. MemType-2L: A Web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM. Biochem. Biophys. Res. Commun., 2007, 360(2), 339-345.
29. Chou, K. C.; Shen, H. B. Recent advances in developing webservers for predicting protein attributes. Nat. Sci., 2009, 1(2), 63-92.