A comprehensive system for identifying internal repeat substructures of proteins

CISIS 2010 - The 4th International Conference on Complex, Intelligent and Software Intensive Systems

Volumn , Issue , 2010, Pages 689-693

  Kao, Hua Ying ^a   Shih, Tsang Huang ^a   Pai, Tun Wen ^a   Lu, Ming Da ^b   Hsu, Hui Huang ^b  

^a NATIONAL TAIWAN OCEAN UNIVERSITY   (Taiwan)

^b TAMKANG UNIVERSITY   (Taiwan)

Author keywords

Internal repeat unit; Length Encoded Secondary Structure; Secondary structure element; Sequence alignment; Solenoid; Structure alignment

Indexed keywords

AMINO ACID SEQUENCE; AUTOCORRELATION ANALYSIS; BENCHMARK DATASETS; BIOLOGICAL FUNCTIONS; COMPREHENSIVE SYSTEM; GENOME EVOLUTION; IDENTIFICATION SYSTEMS; LENGTH ENCODED SECONDARY STRUCTURE; NOVEL METHODS; PROTEIN SEQUENCES; PROTEIN STRUCTURES; QUERY SEQUENCE; SECONDARY STRUCTURE ELEMENT SEQUENCE; SECONDARY STRUCTURE ELEMENTS; SECONDARY STRUCTURES; STRUCTURAL INFORMATION; STRUCTURAL SUPERPOSITIONS; STRUCTURE ALIGNMENT; WEB SYSTEM;

AMINO ACIDS; COMPUTER SOFTWARE; ORGANIC ACIDS; PROTEIN FOLDING; SOLENOIDS;

ALIGNMENT;

EID: 77952727344     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CISIS.2010.92     Document Type: Conference Paper

References (21)

1. Kobe, B. and A. V. Kajava (2000). "When protein folding is simplified to protein coiling: the continuum of solenoid protein structures." Trends Biochem Sci 25(10): 509-515.
2. Heger, A. and L. Holm. "Rapid automatic detection and alignment of repeats in protein sequences." Proteins 41(2): 224-237, 2000.
3. Forrer, P., H. K. Binz, et al. (2004). "Consensus design of repeat proteins." Chembiochem 5(2): 183-189.
4. Andrade, M. A., C. P. Ponting, et al. (2000). "Homology-based method for identification of protein repeats using statistical significance estimates." J Mol Biol 298(3): 521-537.
5. Marcotte, E. M., M. Pellegrini, et al. "A census of protein repeats." Journal of Molecular Biology 293(1): 151-160, 1999.
6. Andrade, M. A., C. Perez-Iratxeta, et al. "Protein repeats: structures, functions, and evolution." J Struct Biol 134(2-3): 117-131, 2001.
7. Saupe, S., B. Turcq, et al. (1995). "A gene responsible for vegetative incompatibility in the fungus Podospora anserina encodes a protein with a GTP-binding motif and G beta homologous domain." Gene 162(1): 135-139.
8. Groves, M. R., N. Hanlon, et al. (1999). "The structure of the protein phosphatase 2A PR65/A subunit reveals the conformation of its 15 tandemly repeated HEAT motifs." Cell 96(1): 99-110.
9. Kurtz, S. and C. Schleiermacher, REPuter: fast computation of maximal repeats in complete genomes. Bioinformatics, 1999. 15(5): p. 426-427
10. Pai, T.-W., Chen, C.-M., Hsiao, M.-C, Chen R., Tzou, W.-S., and Hu C.-H., "An online conserved ssr discovery through cross-species comparison". Computational Biology and Chemistry: Advances and Applications 2: pp. 23-35, 2009.
11. Achaz, G., F. Boyer, et al. "Repseek, a tool to retrieve approximate repeats from large DNA sequences." Bioinformatics 23(1): 119-121, 2007. (Pubitemid 46017864)
12. Abraham, A. L., E. P. C. Rocha, et al. "Swelfe: a detector of internal repeats in sequences and structures." Bioinformatics 24(13): 1536-1537, 2008.
13. George, R. A. and J. Heringa. "The REPRO server: finding protein internal sequence repeats through the Web." Trends Biochem Sci 25(10): 515-517, 2000.
14. Marsella, L., F. Sirocco, et al. (2009). "REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform." Bioinformatics 25(12): i289-295.
15. Henikoff, S. and J. G. Henikoff (1992). "Amino acid substitution matrices from protein blocks." Proc Natl Acad Sci U S A 89(22): 10915-10919.
16. Altschul, S. F., W. Gish, et al. (1990). "Basic local alignment search tool." J Mol Biol 215(3): 403-410.
17. Altschul, S. F., T. L. Madden, et al. (1997). "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs." Nucleic Acids Res 25(17): 3389-3402.
18. Larkin, M. A., G. Blackshields, et al. (2007). "Clustal W and Clustal X version 2.0." Bioinformatics 23(21): 2947-2948.
19. PROPEAT web server. (200910) URL is http://gln.ibms.sinica.edu.tw/ product/repeat/index.html
20. RCSB protein data bank (200910) URL is http://gln.ibms.sinica.edu.tw/ product/repeat/index.html
21. Cheng, J., et al., SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res, 2005. 33(Web Server issue): p. W72-6.