Spine-d: Accurate prediction of short and long disordered regions by a single neural-network based method

Journal of Biomolecular Structure and Dynamics

Volumn 29, Issue 4, 2012, Pages 799-813

  Zhang, Tuo ^a,b,e   Faraggi, Eshel ^a,b,e   Xue, Bin ^c   Dunker, A Keith ^b   Uversky, Vladimir N ^c,d   Zhou, Yaoqi ^a,b  

^a INDIANA UNIVERSITY   (United States)

^b INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF SOUTH FLORIDA   (United States)

^d INSTITUTE FOR BIOLOGICAL INSTRUMENTATION   (Russian Federation)

^e NONE

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTIFICIAL NEURAL NETWORK; CHEMISTRY; PROTEIN TERTIARY STRUCTURE; SENSITIVITY AND SPECIFICITY; ACCURACY; ARTICLE; CONTROLLED STUDY; INTERMETHOD COMPARISON; MOLECULAR RECOGNITION; PREDICTION; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROCESS OPTIMIZATION; RESIDUE ANALYSIS; SENSITIVITY ANALYSIS; STRUCTURE ANALYSIS; VALIDATION PROCESS; X RAY ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; NEURAL NETWORKS (COMPUTER); PROTEIN STRUCTURE, TERTIARY; PROTEINS; SENSITIVITY AND SPECIFICITY;

EID: 84855184716     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/073911012010525022     Document Type: Article

References (63)

1. Uversky, V. N., Oldfield, C. J., and Dunker, A. K., 2005. J Mol Recognit, 18:343–384.
2. Liu, J., Perumal, N. B., Oldfield, C. J., Su, E. W., Uversky, V. N., and Dunker, A. K., 2006. Biochemistry-Us, 45:6873–6888.
3. Galea, C. A., Wang, Y., Sivakolundu, S. G., and Kriwacki, R. W., 2008. Biochemistry-Us, 47:7598–7609.
4. Fuxreiter, M., Tompa, P., Simon, I., Uversky, V. N., Hansen, J. C., and Asturias, F. J., 2008. Nature Chemical Biology, 4:728–737.
5. Dunker, A. K., Cortese, M. S., Romero, P., Iakoucheva, L. M., and Uversky, V. N., 2005. The FEBS Journal, 272:5129–5148.
6. Wright, P. E., and Dyson, H. J., 1999. J Mol Biol, 293:321–331.
7. Xie, H., Vucetic, S., Iakoucheva, L. M., Oldfield, C. J., Dunker, A. K., Uversky, V. N., and Obradovic, Z., 2007. J Proteome Res, 6:1882–1898.
8. Dunker, A. K., Obradovic, Z., Romero, P., Garner, E. C., and Brown, C. J., 2000. Genome informatics. Workshop on Genome Informatics, 11:161–171.
9. Sussman, J. L., Dunker, A. K., Silman, I., and Uversky, V. N., 2008. Curr Opin Struc Biol, 18:756–764.
10. Ward, J. J., Sodhi, J. S., McGuffin, L. J., Buxton, B. F., and Jones, D. T., 2004. J Mol Biol, 337:635–645.
11. Iakoucheva, L. M., Brown, C. J., Lawson, J. D., Obradovic, Z., and Dunker, A. K., 2002. J Mol Biol, 323:573–584.
12. Raychaudhuri, S., Dey, S., Bhattacharyya, N. P., and Mukhopadhyay, D., 2009. PLoS One, 4:e5566
13. Uversky, V. N., Oldfield, C. J., and Dunker, A. K., 2008. Ann Rev Biophys, 37:215–246.
14. Eliezer, D., 2009. Curr Opin Struc Biol, 19:23–30.
15. Longhi, S., Bourhis, J. M., and Canard, B., 2007. Curr Protein Pept Sc, 8:135–149.
16. Turoverov, K. K., Kuznetsova, I. M., and Uversky, V. N., 2010. Prog Biophys Mol Bio, 102:73–84.
17. Uversky, V. N., and Dunker, A. K., 2010. Bba-Proteins Proteom, 1804:1231–1264.
18. Wright, P. E., and Dyson, H. J., 2009. Curr Opin Struc Biol, 19:31–38.
19. Receveur-Brechot, V., Bourhis, J. M., Uversky, V. N., Canard, B., and Longhi, S., 2006. Proteins, 62:24–45.
20. He, B., Wang, K. J., Liu, Y. L., Xue, B., Uversky, V. N., and Dunker, A. K., 2009. Cell Res, 19:929–949.
21. Peng, K., Radivojac, P., Vucetic, S., Dunker, A. K., and Obradovic, Z., 2006. BMC Bioinformatics, 7:208
22. Radivojac, P., Obradovic, Z., Smith, D. K., Zhu, G., Vucetic, S., Brown, C. J., Lawson, J. D., and Dunker, A. K., 2004. Protein Sci, 13:71–80.
23. Romero, P., Obradovic, Z., and Dunker, K., 1997. Genome Informatics. Workshop on Genome Informatics, 8:110–124.
24. Cheng, J. L., Sweredoski, M. J., and Baldi, P., 2005. Data Min Knowl Disc, 11:213–222.
25. Dosztanyi, Z., Csizmok, V., Tompa, P., and Simon, I., 2005. Bioinformatics, 21:3433–3434.
26. Feng, Z. P., Han, P. F., and Zhang, X. Z., 2009. BMC Bioinformatics, 10
27. Hirose, S., Shimizu, K., Kanai, S., Kuroda, Y., and Noguchi, T., 2007. Bioinformatics, 23:2046–2053.
28. Mizianty, M. J., Stach, W., Chen, K., Kedarisetti, K. D., Disfani, F. M., and Kurgan, L., 2010. Bioinformatics, 26:i489–i496.
29. Obradovic, Z., Peng, K., Vucetic, S., Radivojac, P., and Dunker, A. K., 2005. Proteins, 61 (Suppl. 7):176–182.
30. Pollastri, G., Vullo, A., Bortolami, O., and Tosatto, S. C. E., 2006. Nucleic Acids Research, 34:W164–W168.
31. Romero, P., Obradovic, Z., Li, X. H., Garner, E. C., Brown, C. J., and Dunker, A. K., 2001. Proteins-Structure Function and Genetics, 42:38–48.
32. Shimizu, K., Hirose, S., and Noguchi, T., 2007. Bioinformatics, 23:2337–2338.
33. Zhang, T., Faraggi, E., and Zhou, Y. Q., 2010. Proteins, 78:3353–3362.
34. Faraggi, E., Zhang, T., Yang, Y., Kurgan, L., and Zhou, Y., 2012. J Computational Chemistry, doi:10.1002/jcc.21968 (Epub ahead of print)
35. Dor, O., and Zhou, Y., 2007. Proteins, 66:838–845.
36. Faraggi, E., Xue, B., and Zhou, Y., 2009. Proteins, 74:847–856.
37. Schlessinger, A., Punta, M., and Rost, B., 2007. Bioinformatics, 23:2376–2384.
38. Sirota, F. L., Ooi, H. S., Gattermayer, T., Schneider, G., Eisenhaber, F., and Maurer-Stroh, S., 2010. BMC Genomics, 11 (Suppl. 1) S15
39. Vucetic, S., Brown, C. J., Dunker, A. K., and Obradovic, Z., 2003. Proteins, 52:573–584.
40. Sickmeier, M., Hamilton, J. A., LeGall, T., Vacic, V., Cortese, M. S., Tantos, A., Szabo, B., Tompa, P., Chen, J., Uversky, V. N., Obradovic, Z., and Dunker, A. K., 2007. Nucleic Acids Research, 35:D786–793.
41. Schlessinger, A., Punta, M., Yachdav, G., Kajan, L., and Rost, B., 2009. PLoS One, 4
42. Monastyrskyy, B., Fidelis, K., Moult, J., Tramontano, A., and Kryshtafovych, A., 2011. Proteins, 79 (Suppl. 10):107–18.
43. Faraggi, E., Yang, Y. D., Zhang, S. S., and Zhou, Y., 2009. Structure, 17:1515–1527.
44. Zupan, J., 1994. Acta Chimica Slovenica, 41:327–354.
45. Meiler, J., Müller, M., Zeidler, A., and Schmäschke, F., 2001. J Mol Model, 7:360–369.
46. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J. H., Zhang, Z., Miller, W., and Lipman, D. J., 1997. Nucleic Acids Research, 25:3389–3402.
47. Wootton, J. C., 1994. Curr Opin Struc Biol, 4:413–421.
48. Vucetic, S., Obradovic, Z., Vacic, V., Radivojac, P., Peng, K., Iakoucheva, L. M., Cortese, M. S., Lawson, J. D., Brown, C. J., Sikes, J. G., Newton, C. D., and Dunker, A. K., 2005. Bioinformatics, 21:137–140.
49. Noivirt-Brik, O., Prilusky, J., and Sussman, J. L., 2009. Proteins, 77 (Suppl. 9):210–216.
50. McGuffin, L. J., 2008. Bioinformatics, 24:1798–1804.
51. Li, X., Romero, P., Rani, M., Dunker, A. K., and Obradovic, Z., 1999. Genome Informatics. Workshop on Genome Informatics, 10:30–40.
52. Hecker, J., Yang, J. Y., and Cheng, J. L., 2007. BMC Genomics, 9
53. Ward, J. J., Sodhi, J. S., McGuffin, L. J., Buxton, B. F., and Jones, D. T., 2004. J Mol Biol, 337:635–645.
54. Schlessinger, A., Liu, J., and Rost, B., 2007. PLoS Computational Biology, 3:e140
55. Xue, B., Dunbrack, R. L., Williams, R. W., Dunker, A. K., and Uversky, V. N., 2010. Biochimica et Biophysica Acta, 1804:996–1010.
56. Mizianty, M. J., Zhang, T., Xue, B., Zhou, Y. Q., Dunker, A. K., Uversky, V. N., and Kurgan, L., 2011. BMC Bioinformatics, 12
57. Mohan, A., Oldfield, C. J., Radivojac, P., Vacic, V., Cortese, M. S., Dunker, A. K., and Uversky, V. N., 2006. J Mol Biol, 362:1043–1059.
58. Oldfield, C. J., Cheng, Y. G., Cortese, M. S., Romero, P., Uversky, V. N., and Dunker, A. K., 2005. Biochemistry-Us, 44:12454–12470.
59. Vacic, V., Oldfield, C. J., Mohan, A., Radivojac, P., Cortese, M. S., Uversky, V. N., and Dunker, A. K., 2007. J Proteome Res, 6:2351–2366.
60. Cheng, Y., Oldfield, C. J., Meng, J., Romero, P., Uversky, V. N., and Dunker, A. K., 2007. Biochemistry-Us, 46:13468–13477.
61. Garner, E., Romero, P., Dunker, A. K., Brown, C., and Obradovic, Z., 1999. Genome Inform Ser Workshop Genome Inform, 10:41–50.
62. Obradovic, Z., Peng, K., Vucetic, S., Radivojac, P., Brown, C. J., and Dunker, A. K., 2003. Proteins-Structure Function and Genetics, 53:566–572.
63. Le Gall, T., Romero, P. R., Cortese, M. S., Uversky, V. N., and Dunker, A. K., 2007. J Biomol Struct Dyn, 24:325–341.