Length-dependent prediction of protein in intrinsic disorder

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Peng, Kang ^a   Radivojac, Predrag ^b   Vucetic, Slobodan ^a   Dunker, A Keith ^c   Obradovic, Zoran ^a  

^a TEMPLE UNIVERSITY   (United States)

^b INDIANA UNIVERSITY   (United States)

^c INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

10-FOLD CROSS-VALIDATION; AMINO ACID COMPOSITIONS; AMINO ACID SEQUENCE; CRITICAL ASSESSMENT; INTRINSIC DISORDER; INTRINSICALLY DISORDERED PROTEINS; PREDICTION ACCURACY; PROTEIN STRUCTURE PREDICTION;

AMINO ACIDS; EXPERIMENTS; FORECASTING; OPTIMIZATION; STATISTICAL TESTS;

PROTEINS;

ACCURACY; ALGORITHM; AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; PREDICTION; PROTEIN DEFECT; STATISTICAL ANALYSIS; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; MOLECULAR GENETICS; PROCEDURES; PROTEIN SECONDARY STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

PROTEIN;

ALGORITHMS; AMINO ACID SEQUENCE; COMPUTER SIMULATION; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 33745289067     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-208     Document Type: Article

References (73)

1. Dyson HJ, Wright PE: Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 2005, 6:197-208.
2. Wright PE, Dyson HJ: Intrinsically unstructured proteins: reassessing the protein structure-function paradigm. J Mol Biol 1999, 293:321-331.
3. Dunker AK, Lawson JD, Brown CJ, Williams RM, Romero P, Oh JS, Oldfield CJ, Campen AM, Ratliff CM, Hipps KW, et al.: Intrinsically disordered protein. J Mol Graph Model 2001, 19:26-59.
4. Tompa P: Intrinsically unstructured proteins. Trends Biochem Sci 2002, 27:527-533.
5. Uversky VN: What does it mean to be natively unfolded? Eur J Biochem 2002, 269:2-12.
6. Dunker AK, Brown CJ, Lawson JD, Iakoucheva LM, Obradovic Z: Intrinsic disorder and protein function. Biochemistry 2002, 41:6573-6582.
7. Dunker AK, Obradovic Z: The protein trinity - linking function and disorder. Nat Biotechnol 2001, 19:805-806.
8. Uversky VN: Natively unfolded proteins: a point where biology waits for physics. Protein Sci 2002, 11:739-756.
9. Anfinsen CB: Principles that govern the folding of protein chains. Science 1973, 181:223-230.
10. Uversky VN: Protein folding revisited. A polypeptide chain at the folding- misfolding-nonfolding cross-roads: which way to go? Cell Mol Life Sci 2003, 60:1852-1871.
11. Receveur-Brechot V, Bourhis JM, Uversky VN, Canard B, Longhi S: Assessing protein disorder and induced folding. Proteins 2006, 62:24-45.
12. Bychkova VE, Dujsekina AE, Klenin SI, Tiktopulo EI, Uversky VN, Ptitsyn OB: Molten globule-like state of cytochrome c under conditions simulating those near the membrane surface. Biochemistry 1996, 35:6058-6063.
13. Daughdrill GW, Pielak GJ, Uversky VN, Cortese MS, Dunker AK: Natively disordered proteins. In Protein Folding Handbook Edited by: Buchner J, Kiefhaber T. Weinheim, Wiley-VCH; 2005:271-353.
14. Rose GD: Unfolded Proteins. In Advances in Protein Chemistry Volume 62. Edited by: Richards FM, Eisenerg DS, Kuriyan J. New York:Academic Press; 2002.
15. Romero P, Obradovic Z, Dunker AK: Sequence data analysis for long disordered regions prediction in the calcineurin family. Genome Inform Ser Workshop Genome Inform 1997, 8:110-124.
16. Romero P, Obradovic Z, Kissinger CR, Villafranca JE, Dunker AK: Identifying disordered regions in proteins from amino acid sequences. In Proceedings of IEEE International Conference on Neural Networks Houston TX; 1997:90-95.
17. Uversky VN, Gillespie JR, Fink AL: Why are "natively unfolded" proteins unstructured under physiologic conditions? Proteins 2000, 41:415-427.
18. Romero P, Obradovic Z, Li X, Garner EC, Brown CJ, Dunker AK: Sequence complexity of disordered protein. Proteins 2001, 42:38-48.
19. Vucetic S, Brown CJ, Dunker AK, Obradovic Z: Flavors of protein disorder. Proteins 2003, 52:573-584.
20. Linding R, Russell RB, Neduva V, Gibson TJ: GlobPlot: exploring protein sequences for globularity and disorder. Nucleic Acids Res 2003, 31:3701-3708.
21. Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB: Protein disorder prediction: Implications for structural proteomics. Structure (Camb) 2003, 11:1453-1459.
22. Liu J, Rost B: NORSp: predictions of long regions without regular secondary structure. Nucleic Acids Res 2003, 31:3833-3835.
23. Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT: Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 2004, 337:635-645.
24. Peng K, Vucetic S, Radivojac P, Brown CJ, Dunker AK, Obradovic Z: Optimizing long intrinsic disorder predictors with protein evolutionary information. J Bio inform Comput Biol 2005, 3:35-60.
25. Oldfield CJ, Cheng Y, Cortese MS, Brown CJ, Uversky VN, Dunker AK: Comparing and combining predictors of mostly disordered proteins. Biochemistry 2005, 44:1989-2000.
26. Coeytaux K, Poupon A: Prediction of unfolded segments in a protein sequence based on amino acid composition. Bioinformatics 2005, 21:1891-1900.
27. Dosztanyi Z, Csizmok V, Tompa P, Simon I: The pair wise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. J Mol Biol 2005, 347:827-839.
28. Yang ZR, Thomson R, McNeil P, Esnouf RM: RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics 2005, 21:3369-3376.
29. Cheng J, Sweredoski M, Baldi P: Accurate prediction of protein disordered regions by mining protein structure data. Data Mining and Knowledge Discovery 2005, 11:213-222.
30. Bracken C, akoucheva LM, Romero PR, Dunker AK: Combining prediction, computation and experiment for the characterization of protein disorder. Curr Opin Struct Biol 2004, 14:570-576.
31. Iakoucheva LM, Brown CJ, Lawson JD, Obradovic Z, Dunker AK: Intrinsic disorder in cell-signaling and cancer-associated proteins. J Mol Biol 2002, 323:573-584.
32. Iakoucheva LM, Radivojac P, Brown CJ, O'Connor TR, Sikes JG, Obradovic Z, Dunker AK: The Importance of Intrinsic disorder for protein phosphorylation. Nucleic Acids Res 2004, 32:1037-1049.
33. Oldfield CJ, Ulrich EL, Cheng Y, Dunker AK, Markley JL: Addressing the intrinsic disorder bottleneck in structural proteomics. Proteins 2005, 59:444-453.
34. Peti W, Etezady-Esfarjani T, Herrmann T, Klock HE, Lesley SA, Wuthrich K: NMR for structural proteomics of Thermotoga maritima: screening and structure determination. J Struct Funct Genomics 2004, 5:205-215.
35. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
36. Radivojac P, Obradovic Z, Brown CJ, Dunker AK: Improving sequence alignments for intrinsically disordered proteins. In Proceedings of Pacific Symposium on Biocomputing 3-7 January Lihue, Hawaii, USA; 2002:589-600.
37. Brown CJ, Takayama S, Campen AM, Vise P, Marshall T, Oldfield CJ, Williams CJ, Dunker AK: Evolutionary rate heterogeneity in proteins with long disordered regions. J Mol Evol 2002, 55:104-110.
38. Dunker AK, Brown CJ, Obradovic Z: Identification and functions of usefully disordered proteins. Adv Protein Chem 2002, 62:25-49.
39. Radivojac P, Obradovic Z, Smith DK, Zhu G, Vucetic S, Brown CJ, Lawson JD, Dunker AK: Protein flexibility and intrinsic disorder. Protein Sci 2004, 13:71-80.
40. Obradovic Z, Peng K, Vucetic S, Radivojac P, Brown CJ, Dunker AK: Predicting intrinsic disorder from amino acid sequence. Proteins 2003, 53(Suppl 6):566-572.
41. Obradovic Z, Peng K, Vucetic S, Radivojac P, Dunker AK: Exploiting heterogeneous sequence properties improves prediction of protein disorder. Proteins 2005, 61 (Suppl 7):176-182.
42. Jin Y, Dunbrack RLJ: Assessment of disorder predictions in CASP6. Proteins 2005, 61 (Suppl 7):167-175.
43. Vapnik V: Statistical Learning Theory New York: John Wiley & Sons; 1998.
44. Davidson R, MacKinnon J: Estimation and Inference in Econometrics New York: Oxford University Press; 1993.
45. Vucetic S, Obradovic Z, Vacic V, Radivojac P, Peng K, Iakoucheva LM, Cortese MS, Lawson JD, Brown CJ, Sikes JG, et al.: DisProt: a database of protein disorder. Bioinformatics 2005, 21:137-140.
46. Smith DK, Radivojac P, Obradovic Z, Dunker AK, Zhu G: Improved amino acid flexibility parameters. Protein Sci 2003, 12:1060-1072.
47. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
48. Jones DT: Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999, 292:195-202.
49. Jones DT, Ward JJ: Prediction of disordered regions in proteins from position specific score matrices. Proteins 2003, 53(Suppl 6):573-578.
50. Rost B, Sander C: Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 1994, 19:55-72.
51. Wootton JC, Federhen S: Statistics of local complexity in amino acid sequences and sequence databases. Comput Chem 1993, 17:149-163.
52. Kyte J, Doolittle RF: A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982, 157:105-132.
53. Vihinen M, Torkkila E, Riikonen P: Accuracy of protein flexibility predictions. Proteins 1994, 19:141-149.
54. Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, et al.: The Universal Protein Resource (UniProt). Nucleic Acids Res 2005, 33:D154-D159.
55. Radivojac P, Obradovic Z, Dunker AK, Vucetic S: Feature selection filters based on the permutation test. In Proceedings of 15th European Conference on Machine Learning Pisa, Italy; 2004:334-346.
56. Witten IH, Frank E: Data Mining: Practical Machine Learning Tools and Techniques 2nd edition. San Francisco: Morgan Kaufmann; 2005.
57. Noble WS, et al.: Support vector machine applications in computational biology. In Kemal Methods in Computational Biology Volume 14. Edited by: Schoelkopf B, Tsuda K, Vert JP. MIT Press; 2004:71-92.
58. Joachims T: Making large-scale SVM learning practical. In Advances in Kernel Methods - Support Vector Learning Edited by: Schoelkopf B, Burges C, Smola A. Cambridge, MA: MIT Press; 1999.
59. Platt JC: Probabilistic outputs for support vector machines and comparison to regularized likelihood methods. In Advances in Large Margin Classifiers Edited by: Smola AJ, Bartlett P, Scholkopf B, Schuurmans D. MIT Press; 1999:61-74.
60. Bishop CM: Neural Networks for Pattern Recognition Oxford, UK: Oxford University Press; 1995.
61. Breiman L: Bagging predictors. Mach Learn 1996, 24:123-140.
62. Melamud E, Moult J: Evaluation of disorder predictions in CASP5. Proteins 2003, 53(Suppl 6):561-565.
63. Matthews BW: Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta 1975, 405:442-451.
64. Hanley JA, McNeil BJ: A method of comparing the areas under receiver operating characteristic curves derived from the same cases. Radiology 1983, 148:839-843.
65. Efron B, Tibshirani RJ: An Introduction to the Bootstrap New York: Chapman & Hall; 1993.
66. Prilusky J, Felder CE, Zeev-Ben-Mordehai T, Rydberg EH, Man O, Beckmann JS, Simian I, Sussman JL: Fold Index: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics 2005, 21:3435-3438.
67. She M, Decker CJ, Chen N, Tumati S, Parker R, Song H: Crystal structure and functional analysis of Dcp2p from Schizosaccharomyces pombe. Nat Struct Mol Biol 2006, 13:63-70.
68. de la Sierra-Gallay IL, Pellegrini O, Condon C: Structural basis for substrate binding, cleavage and allostery in the tRNA maturase R Nase Z. Nature 2005, 433:657-661.
69. Ehebauer MT, Chirgadze DY, Hayward P, Martinez-Arias A, Blundell TL: High-resolution crystal structure of the human Notch 1 ankyrin domain. Biochem J 2005, 392:13-20.
70. Gunasekaran K, Tsai CJ, Nussinov R: Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers. J Mol Biol 2004, 341:1327-1341.
71. Cuff JA, Clamp ME, Siddiqui AS, Finlay M, Barton GJ: Jpred: a consensus secondary structure prediction server. Bioinformatics 1998, 14:892-893.
72. Bradley CM, Barrick D: Limits of cooperativity in a structurally modular protein: response of the Notch ankyrin domain to analogous alanine substitutions in each repeat. J Mol Biol 2002, 324:373-386.
73. Garner E, Cannon P, Romero P, Obradovic Z, Dunker AK: Predicting disordered regions from amino acid sequence: common themes despite differing structural characterization. Genome Inform Ser Workshop Genome Inform 1998, 9:201-213.