Subclassifying disordered proteins by the CH-CDF plot method

Pacific Symposium on Biocomputing

Volumn , Issue , 2012, Pages 128-139

  Huang, Fei ^a   Oldfield, Christopher ^a   Meng, Jingwei ^a   Hsu, Wei Lun ^a   Xue, Bin ^a,b   Uversky, Vladimir N ^a,b   Romero, Pedro ^a   Dunker, A Keith ^a  

^a INDIANA UNIVERSITY   (United States)

^b UNIVERSITY OF SOUTH FLORIDA   (United States)

Author keywords

CDF prediction; CH plot; Classification; Intrinsically disordered protein

Indexed keywords

CLASSIFICATION (OF INFORMATION); DISTRIBUTION FUNCTIONS;

BIOLOGICAL FUNCTIONS; CH PLOT; CUMULATIVE DISTRIBUTION FUNCTION; DISORDERED PROTEINS; DISORDERED REGIONS; FUNCTIONAL SEPARATIONS; INTRINSICALLY DISORDERED PROTEINS; SIGNALING PATHWAYS;

PROTEINS;

PROTEIN; PROTEOME;

ALGORITHM; AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BIOLOGY; CHEMISTRY; CLASSIFICATION; GENETICS; MOUSE; PROTEIN CONFORMATION; PROTEIN DATABASE; STRUCTURAL HOMOLOGY;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MICE; PROTEIN CONFORMATION; PROTEINS; PROTEOME; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 84891464898     PISSN: 23356928     EISSN: 23356936     Source Type: Journal    
DOI: None     Document Type: Conference Paper

References (20)

1. Dunker, A. K., C. J. Brown and Z. Obradovic (2002). "Identification and functions of usefully disordered proteins." Adv Protein Chem 62: 25-49.
2. Oldfield, C. J., Y. Cheng, M. S. Cortese, C. J. Brown, V. N. Uversky and A. K. Dunker (2005). "Comparing and combining predictors of mostly disordered proteins." Biochemistry 44(6): 1989-2000.
3. Iakoucheva, L. M., C. J. Brown, J. D. Lawson, Z. Obradovic and A. K. Dunker (2002). "Intrinsic disorder in cell-signaling and cancer-associated proteins." J Mol Biol 323(3): 573-84.
4. Xie, H., S. Vucetic, L. M. Iakoucheva, C. J. Oldfield, A. K. Dunker, V. N. Uversky and Z. Obradovic (2007). "Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions." J Proteome Res 6(5): 1882-98.
5. Vucetic, S., H. Xie, L. M. Iakoucheva, C. J. Oldfield, A. K. Dunker, Z. Obradovic and V. N. Uversky (2007). "Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions." J Proteome Res 6(5): 1899-916.
6. Xie, H., S. Vucetic, L. M. Iakoucheva, C. J. Oldfield, A. K. Dunker, Z. Obradovic and V. N. Uversky (2007). "Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins." J Proteome Res 6(5): 1917-32.
7. Murzin, A. G., S. E. Brenner, T. Hubbard and C. Chothia (1995). "SCOP: a structural classification of proteins database for the investigation of sequences and structures." J Mol Biol 247(4): 536-40.
8. Orengo, C. A., A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells and J. M. Thornton (1997). "CATH-a hierarchic classification of protein domain structures." Structure 5(8): 1093-108.
9. Reeck, G. R., C. de Haen, D. C. Teller, R. F. Doolittle, W. M. Fitch, R. E. Dickerson, P. Chambon, A. D. McLachlan, E. Margoliash, T. H. Jukes and et al. (1987). ""Homology" in proteins and nucleic acids: a terminology muddle and a way out of it." Cell 50(5): 667.
10. Vucetic, S., C. J. Brown, A. K. Dunker and Z. Obradovic (2003). "Flavors of protein disorder." Proteins 52(4): 573-84.
11. Uversky, V. N. and A. K. Dunker "Understanding protein non-folding." Biochim Biophys Acta 1804(6): 1231-64.
12. Uversky, V. N., J. R. Gillespie and A. L. Fink (2000). "Why are "natively unfolded" proteins unstructured under physiologic conditions?" Proteins 41(3): 415-27.
13. Oldfield, C.J., Cheng, Y., Cortese, M.S., Brown, C.J., Uversky, V.N., and Dunker, A.K. Comparing and combining predictors of mostly disordered proteins. Biochemistry. 44:1989-2000 (2005).
14. Xue, B., C. J. Oldfield, A. K. Dunker and V. N. Uversky (2009). "CDF it all: consensus prediction of intrinsically disordered proteins based on various cumulative distribution functions." FEBS Lett 583(9): 1469-74.
15. Le Gall, T., P.R. Romero, M.S. Cortese, V.N. Uversky, and A.K. Dunker. "Intrinsic disorder in the Protein Data Bank." J Biomol Struct Dyn 24(4): 325-42 (2007).
16. Mohan, A., Sullivan, Jr., W.J., Radivojac, P., Dunker, A.K., and Uversky, V.N. "Intrinsic disorder in pathogenic and non-pathogenic microbes: discovering and analyzing the unfoldome of early-branching eukaryotes." Molecular Biosystems 4: 328-340 (2008).
17. Xue, B. C.J. Oldfield, Y.Y. Van, A.K. Dunker, and V.N. Uversky. "Protein intrinsic disorder and induced pluripotent stem cells." Mol Biosystems (In Press)
18. Sun, Z., B. Xue, W.T. Jones, E. Rikkerink, A.K. Dunker, and V.N. Uversky. "A functionally required unfoldome from the plant kingdom: intrinsically disordered N-terminal domains of GRAS proteins are involved in molecular recognition during plant development." Plant Mol. Biol. (In Press).
19. Obradovic, Z., K. Peng, S. Vucetic, P. Radivojac and A. K. Dunker (2005). "Exploiting heterogeneous sequence properties improves prediction of protein disorder." Proteins 61 Suppl 7: 176-82.
20. Magrane, M. and U. Consortium "UniProt Knowledgebase: a hub of integrated protein data." Database (Oxford) 2011: bar009.