D2P2: Database of disordered protein predictions

Nucleic Acids Research

Volumn 41, Issue D1, 2013, Pages

  Oates, Matt E ^a   Romero, Pedro ^b   Ishida, Takashi ^c   Ghalwash, Mohamed ^d,e   Mizianty, Marcin J ^f   Xue, Bin ^g   Dosztányi, Zsuzsanna ^h   Uversky, Vladimir N ^g,i   Obradovic, Zoran ^d   Kurgan, Lukasz ^f   Dunker, A Keith ^b   Gough, Julian ^a  

^a UNIVERSITY OF BRISTOL   (United Kingdom)

^b INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^d Temple University   (United States)

^e Ain Shams University   (Egypt)

^f UNIVERSITY OF ALBERTA   (Canada)

^g UNIVERSITY OF SOUTH FLORIDA   (United States)

^h INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

ⁱ INSTITUTE FOR BIOLOGICAL INSTRUMENTATION   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; DATABASE OF DISORDERED PROTEIN PREDICTION; INTERNET; PREDICTION; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN STRUCTURE; TREE OF LIFE;

DATABASES, PROTEIN; GENOME; INTERNET; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE ANALYSIS, PROTEIN;

EID: 84876524220     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1226     Document Type: Article

References (42)

1. Uversky, V.N., Gillespie, J.R. and Fink, A.L. (2000) Why are "natively unfolded" proteins unstructured under physiologic conditions? Proteins, 41, 415-427.
2. Uversky, V.N. (2002) Natively unfolded proteins: a point where biology waits for physics. Protein Sci., 11, 739-756.
3. Iakoucheva, L.M., Radivojac, P., Brown, C.J., O'Connor, T.R., Sikes, J.G., Obradovic, Z. and Dunker, A.K. (2004) The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res., 32, 1037-1049.
4. Song, J., Lee, M.S., Carlberg, I., Vener, A.V. and Markley, J.L. (2006) Micelle-induced folding of spinach thylakoid soluble phosphoprotein of 9 kDa and its functional implications. Biochemistry, 45, 15633-15643.
5. Yamada, J., Phillips, J.L., Patel, S., Goldfien, G., Calestagne-Morelli, A., Huang, H., Reza, R., Acheson, J., Krishnan, V.V., Newsam, S. et al. (2010) A bimodal distribution of two distinct categories of intrinsically-disordered structures with separate functions in FG nucleoporins. Mol. Cell. Proteomics, 9, 2205-2224.
6. Dunker, A.K., Silman, I., Uversky, V.N. and Sussman, J.L. (2008) Function and structure of inherently disordered proteins. Curr. Opin. Struct. Biol., 18, 756-764.
7. Dyson, H.J. and Wright, P.E. (2005) Intrinsically unstructured proteins and their functions. Nat. Rev. Mol. Cell Biol., 6, 197-208.
8. Rose, P.W., Beran, B., Bi, C., Bluhm, W.F., Dimitropoulos, D., Goodsell, D.S., Prlic, A., Quesada, M., Quinn, G.B., Westbrook, J.D. et al. (2011) The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res., 39, D392-D401.
9. Sickmeier, M., Hamilton, J.A., LeGall, T., Vacic, V., Cortese, M.S., Tantos, A., Szabo, B., Tompa, P., Chen, J., Uversky, V.N. et al. (2007) DisProt: the database of disordered proteins. Nucleic Acids Res., 35, D786-D793.
10. Fukuchi, S., Sakamoto, S., Nobe, Y., Murakami, S.D., Amemiya, T., Hosoda, K., Koike, R., Hiroaki, H. and Ota, M. (2012) IDEAL: intrinsically disordered proteins with extensive annotations and literature. Nucleic Acids Res., 40, D507-D511.
11. Di Domenico, T., Walsh, I., Martin, A.J.M. and Tosatto, S.C.E. (2012) MobiDB: a comprehensive database of intrinsic protein disorder annotations. Bioinformatics, 28, 2080-2081.
12. Martin, A.J.M., Walsh, I. and Tosatto, S.C.E. (2010) MOBI: a web server to define and visualize structural mobility in NMR protein ensembles. Bioinformatics, 26, 2916-2917.
13. He, B., Wang, K., Liu, Y.-L., Xue, B., Uversky, V.N. and Dunker, A.K. (2009) Predicting intrinsic disorder in proteins: an overview. Cell Res., 19, 929-949.
14. Peng, Z.L. and Kurgan, L. (2012) Comprehensive comparative assessment of in-silico predictors of disordered regions. Curr. Protein Pept. Sci., 13, 6-18.
15. Romero, P., Obradovic, Z., Kissinger, C., Villifranca, J.E. and Dunker, A.K. (1997) Identifying disordered regions in proteins from amino acid sequence. Proc. Int. Conf. Neural Networks, 1, 90-95.
16. Peng, K., Radivojac, P., Vucetic, S., Dunker, A.K. and Obradovic, Z. (2006) Length-dependent prediction of protein intrinsic disorder. BMC Bioinformatics, 7, 208.
17. Kozlowski, L.P. and Bujnicki, J.M. (2012) MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins. BMC Bioinformatics, 13, 111.
18. Fukuchi, S., Homma, K., Minezaki, Y., Gojobori, T. and Nishikawa, K. (2009) Development of an accurate classification system of proteins into structured and unstructured regions that uncovers novel structural domains. BMC Struct. Biol., 9, 26.
19. Ward, J.J., Sodhi, J.S., McGuffin, L.J., Buxton, B.F. and Jones, D.T. (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J. Mol. Biol., 337, 635-645.
20. Romero, P., Obradovic, Z., Li, X., Garner, E.C., Brown, C.J. and Dunker, A.K. (2001) Sequence complexity of disordered protein. Proteins, 42, 38-48.
21. Li, X., Romero, P., Rani, M., Dunker, A.K. and Obradovic, Z. (1999) Predicting protein disorder for N-, C-, and internal regions. Genome Inform Ser Workshop Genome Inform, 10, 30-40.
22. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
23. Rost, B., Sander, C. and Schneider, R. (1994) PHD - an automatic mail server for protein secondary structure prediction. Comput. Appl. Biosci., 10, 53-60.
24. Jones, D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
25. Xue, B., Dunbrack, R.L., Williams, R.W., Dunker, A.K. and Uversky, V.N. (2010) PONDR-FIT: a meta-predictor of intrinsically disordered amino acids. Biochem. Biophys. Acta, 1804, 996-1010.
26. Chen, J.W., Romero, P., Uversky, V.N. and Dunker, A.K. (2006) Conservation of intrinsic disorder in protein domains and families: I. A database of conserved predicted disordered regions. J. Proteome Res., 5, 879-887.
27. Ishida, T. and Kinoshita, K. (2007) PrDOS: prediction of disordered protein regions from amino acid sequence. Nucleic Acids Res., 35, W460-W464.
28. Ghalwash, M.F., Dunker, A.K. and Obradovic, Z. (2012) Uncertainty analysis in protein disorder prediction. Mol. Biosyst., 8, 381-391.
29. Monastyrskyy, B., Fidelis, K., Moult, J., Tramontano, A. and Kryshtafovych, A. (2011) Evaluation of disorder predictions in CASP9. Proteins: Struct., Funct., Bioinf., 79, 107-118.
30. Walsh, I., Martin, A.J., Di Domenico, T. and Tosatto, S.C. (2012) ESpritz: accurate and fast prediction of protein disorder. Bioinformatics, 28, 503-509.
31. Dosztányi, Z., Csizmók, V., Tompa, P. and Simon, I. (2005) The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. J. Mol. Biol., 347, 827-839.
32. Mészáros, B., Simon, I. and Dosztanyi, Z. (2009) Prediction of protein binding regions in disordered proteins. PLoS Comput. Biol., 5, e1000376.
33. Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001) Assignment of homology to genome sequences using a library of hidden Markov Models that represent all proteins of known structure. J. Mol. Biol., 313, 903-919.
34. de Lima Morais, D., Fang, H., Rackham, O., Wilson, D., Pethica, R., Chothia, C. and Gough, J. (2011) SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucleic Acids Res., 39, D427-D434.
35. Murzin, A.G., Brenner, S.E., Hubbard, T. and Chothia, C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
36. Andreeva, A., Howorth, D., Brenner, S.E., Hubbard, T.J.P., Chothia, C. and Murzin, A.G. (2004) SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res., 32, D226-D229.
37. Biegert, A. and Soding, J. (2009) Sequence context-specific profiles for homology searching. Proc. Natl Acad. Sci. USA., 106, 3770-3775.
38. Hornbeck, P.V., Kornhauser, J.M., Tkachev, S., Zhang, B., Skrzypek, E., Murray, B., Latham, V. and Sullivan, M. (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res., 40, D261-D270.
39. Peng, Z. and Kurgan, L. (2012) On the complementarity of the consensus-based disorder prediction. Pac. Symp. Biocomput., 176-187.
40. Fukuchi, S., Hosoda, K., Homma, K., Gojobori, T. and Nishikawa, K. (2011) Binary classification of protein molecules into intrinsically disordered and ordered segments. BMC Struct. Biol., 11:29.
41. Chen, J.W., Romero, P., Uversky, V.N. and Dunker, A.K. (2006) Conservation of intrinsic disorder in protein domains and families: II. Functions of conserved disorder. J. Proteome Res., 5, 888-898.
42. Ellis, J.D., Barrios-Rodiles, M., Colak, R., Irimia, M., Kim, T., Calarco, J.A., Wang, X., Pan, Q., O'Hanlon, D., Kim, P.M. et al. (2012) Tissue-specific alternative splicing remodels protein-protein interaction networks. Mol. Cell., 46, 884-892.