A neural network for predicting protein disorder using amino acid hydropathy values

Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '05

Volumn 2005, Issue , 2005, Pages

  Stoffer, Deborah A ^a   Volkert, L Gwenn ^a  

^a KENT STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; JAVA PROGRAMMING LANGUAGE; NEURAL NETWORKS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; STATISTICAL METHODS; X RAY CRYSTALLOGRAPHY;

CIRCULAR DICHROISM; DISCRIMINANT ANALYSIS; HYDROPATHY VALUES; PROTEASE DIGESTION; SUPPORT VECTOR MACHINES (SVM);

PROTEINS;

EID: 33847192813     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/cibcb.2005.1594958     Document Type: Conference Paper

References (36)

1. C. A. Orengo, A. E. Todd, and J. M. Thornton, "From protein structure to function," Current Opinion in Structural Biology, vol. 9, no. 3, pp. 374-382, 1999.
2. P. Tompa, "Intrinsically unstructured proteins," Trends in Biochemical Sciences, vol. 27, no. 10, pp. 527-533, 2002.
3. P. E. Wright and H. J. Dyson, "Intrinsically unstructured proteins: reassessing the protein structure-function paradigm," Journal of Molecular Biology, vol. 293, no. 2, pp. 321-331, 1999.
4. A. K. Dunker, C. J. Brown, J. D. Lawson, L. M. Iakoucheva, and Z. Obradovic, "Intrinsic disorder and protein function," Biochemistry, vol. 41, no. 21, pp. 6573-6582, 2002.
5. A. K. Dunker, J. D. Lawson, C. J. Brown, R. M. Williams, P. Romero, J. S. Oh, C. J. Oldfield, A. M. Campen, C. M. Ratliff, K. W. Hipps, J. Ausio, M. S. Nissen, R. Reeves, C. Kang, C. R. Kissinger, R. W. Bailey, M. D. Griswold, W. Chiu, E. C. Garner, and Z. Obradovic, "Intrinsically disordered protein," Journal of Molecular Graphics and Modelling, vol. 19, no. 1, pp. 26-59, 2001.
6. V. N. Uversky, "Natively unfolded proteins: a point where biology waits for physics," Protein Science, vol. 11, no. 4, pp. 739-756, 2002.
7. A. K. Dunker, Z. Obradovic, P. Romero, E. C. Garner, and C. J. Brown, "Intrinsic protein disorder in complete genomes," Genome. Informatics Series: Workshop on Genome Informatics, vol. 11, pp. 161-171, 2000.
8. P. Romero, Z. Obradovic, X. Li, E. C. Garner, C. J. Brown, and A. K. Dunker, "Sequence complexity of disordered protein," Proteins, vol. 42, no. 1, pp. 38-48, 2001.
9. C. Bracken, L. M. Iakoucheva, P. R. Romero, and A. K. Dunker, "Combining prediction, computation and experiment for the characterization of protein disorder," Current Opinion in Structural Biology, vol. 14, no. 5, pp. 570-576, 2004.
10. S. Vucetic, C. J. Brown, A. K. Dunker, and Z. Obradovic, "Flavors of protein disorder," Proteins, vol. 52, no. 4, pp. 573-584, 2003.
11. H. J. Dyson and P. E. Wright, "Unfolded proteins and protein folding studied by nmr," Chemical Reviews, vol. 104, no. 8, pp. 3607-3622, 2004.
12. E. Garner, P. Cannon, P. Romero, Z. Obradovic, and A. K. Dunker, "Predicting disordered regions from amino acid sequence: Common themes despite differing structural characterization," Genome Informatics Series: Workshop on Genome Informatics, vol. 9, pp. 201-213, 1998.
13. R. M. Williams, Z. Obradovi, V. Mathura, W. Braun, E. C. Garner, J. Young, S. Takayama, C. J. Brown, and A. K. Dunker, "The protein non-folding problem: amino acid determinants of intrinsic order and disorder," Pacific Symposium on Biocomputing, pp. 89-100, 2001.
14. L. M. Iakoucheva and A. K. Dunker, "Order, disorder, and flexibility: prediction from protein sequence," Structure (Camb), vol. 11, no. 11, pp. 1316-1317, 2003.
15. X. Li, Z. Obradovic, C. J. Brown, E. C. Garner, and A. K. Dunker, "Comparing predictors of disordered protein," Genome. Informatics Series: Workshop on Genome Informatics, vol. 11, pp. 172-184, 2000.
16. P. Romero, Z. Obradovi, and A. K. Dunker, "Intelligent data analysis for protein disorder prediction," Artificial Intelligence Review, vol. 14, no. 6, S2, pp. 447-484, 2000.
17. L. M. Iakoucheva, C. J. Brown, J. D. Lawson, Z. Obradovic, and A. K. Dunker, "Intrinsic disorder in cell-signaling and cancer-associated proteins," Journal of Molecular Biology, vol. 323, no. 3, pp. 573-584, 2002.
18. Z. Obradovic, K. Peng, S. Vucetic, P. Radivojac, C. J. Brown, and A. K. Dunker, "Predicting intrinsic disorder from amino acid sequence," Proteins, vol. 53 Suppl 6, pp. 566-572, 2003.
19. R. Linding, L. J. Jensen, F. Diella, P. Bork, T. J. Gibson, and R. B. Russell, "Protein disorder prediction: implications for structural proteomics," Structure (Comb), vol. 11, no. 11, pp. 1453-1459, 2003.
20. P. Radivojac, Z. Obradovic, D. K. Smith, G. Zhu, S. Vucetic, C. J. Brown, J. D. Lawson, and A. K. Dunker, "Protein flexibility and intrinsic disorder," Protein Science, vol. 13, no. 1, pp. 71-80, 2004.
21. P. Romero, Z. Obradovic, C. Kissinger, J. E. Villafranca, and A. K. Dunker, "Identifying disordered regions in proteins from amino acid sequence," Proceedings IEEE International Conference on Neural Networks, vol. 1, pp. 90-95, 1997.
22. X. Li, P. Romero, M. Rani, A. K. Dunker, and Z. Obradovic, "Predicting protein disorder for n-, c-, and internal regions," Genome Informatics Series: Workshop on Genome Informatics, vol. 10, pp. 30-40, 1999.
23. S. Lise and D. T. Jones, "Sequence patterns associated with disordered regions in proteins," Proteins, vol. 58, no. 1, pp. 144-150, 2005.
24. P. Romero, Z. Obradovic, C. R. Kissinger, J. E. Villafranca, E. Garner, S. Guilliot, and A. K. Dunker, "Thousands of proteins likely to have long disordered regions," Pacific Symposium on Biocomputing, pp. 437-448, 1998.
25. S. Vucetic, P. Radivojac, Z. Obradovi, C. J. Brown, and A. K. Dunker, "Methods for improving protein disorder prediction," Proc. 2001 IEEE/INNS International Joint Conference on Neural Networks, vol. 4, pp. 2718-2723, 2001.
26. K. Peng, S. Vucetic, P. Radivojac, C. J. Brown, A. K. Dunker, and Z. Obradovic, "Optimizing long intrinsic disorder predictors with protein evolutionary information," Journal of Bioinformatics and Computational Biology, vol. 3, no. 1, pp. 35-60, 2005.
27. R. Thomson, T. C. Hodgman, Z. R. Yang, and A. K. Doyle, "Characterizing proteolytic cleavage site activity using bio-basis function neural networks," Bioinformatics, vol. 19, no. 14, pp. 1741-1747, 2003.
28. D. T. Jones and J. J. Ward, "Prediction of disordered regions in proteins from position specific score matrices," Proteins, vol. 53 Suppl 6, pp. 573-578, 2003.
29. E. A. Weathers, M. E. Paulaitis, T. B. Woolf, and J. H. Hoh, "Reduced amino acid alphabet is sufficient to accurately recognize intrinsically disordered protein," FEBS Letters, vol. 576, no. 3, pp. 348-352, 2004.
30. J. J. Ward, J. S. Sodhi, L. J. McGuffin, B. F. Buxton, and D. T. Jones, "Prediction and functional analysis of native disorder in proteins from the three kingdoms of life," Journal of Molecular Biology, vol. 337, no. 3, pp. 635-645, 2004.
31. R. Linding, R. B. Russell, V. Neduva, and T. J. Gibson, "Globplot: Exploring protein sequences for globularity and disorder," Nucleic Acids Research, vol. 31, no. 13, pp. 3701-3708, 2003.
32. J. J. Ward, L. J. McGuffin, K. Bryson, B. F. Buxton, and D. T. Jones, "The disopred server for the prediction of protein disorder," Bioinformatics, vol. 20, no. 13, pp. 2138-2139, 2004.
33. V. N. Uversky, J. Gillespie, and A. L. Fink, "Why are 'natively unfolded' proteins unstructured under the phsiological conditions'?" Proteins, vol. 42, no. 3, pp. 415-427, 2000.
34. S. Vucetic, Z. Obradovic, V. Vacic, P. Radivojac, K. Peng, L. M. Iakoucheva, M. S. Cortese, J. D. Lawson, C. J. Brown, J. G. Sikes, C. D. Newton, and A. K. Dunker, "Disprot: a database of protein disorder," Bioinformatics, vol. 21, no. 1, pp. 137-140, 2005.
35. J. Kyte and R. F. Doolittle, "A simple method for displaying the hydropathic character of a protein," Journal of Molecular Biology, vol. 157, no. 1, pp. 105-132, 1982.
36. M. Riedmiller and H. Braun, "A direct adaptive method for faster backpropagation learning: The rprop algorithm," in Proceedings of the IEEE International Conference on Neural Networks, San Fransisco, CA, 1993, pp. 586-591.