Russian version English version
Volume 5   Issue 2   Year 2010
Lobanov M.Yu., Galzitskaya O.V.

Statistical Analysis and Prediction of Disordered Residues in Protein Structures

Mathematical Biology & Bioinformatics. 2010;5(2):124-137.

doi: 10.17537/2010.5.124.

References

  1. Tompa P. Intrinsically unstructured proteins. Trends Biochem. Sci. 2002;27:527-533. doi: 10.1016/S0968-0004(02)02169-2
  2. Wright PE, Dyson HJ. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J. Mol. Biol. 1999;293:321-331.
  3. Sickmeier M, Hamilton JA, LeGall T, Vacic V, Cortese MS, Tantos A, Szabo B, Tompa P, Chen J, Uversky VN, Obradovic Z, Dunker AK. DisProt: the database of disordered proteins. Nucl. Acids Res. 2007;35:D786-793. doi: 10.1093/nar/gkl893
  4. Dunker AK, Brown CJ, Lawson JD, Iakoucheva LM, Obradovic Z. Intrinsic disorder and protein function. Biochemistry. 2002;41:6573-6582. doi: 10.1021/bi012159+
  5. Romero P, Obradovic Z, Kissinger CR, Villafranca LE, Dunker AK. Identifying disordered regions in proteins from amino acid sequence. In: Proc. of the IEE International Conference on Neural Networks. 1997. P. 90-95.
  6. Li X, Romero P, Rani M, Dunker AK, Obradovic AZ. Prediction protein disordered for N-, C-, and internal regions. Genome Inform. 1999;10:30-40.
  7. Galzitskaya OV, Garbuzynskiy SO, Lobanov MYu. Prediction of amyloidogenic and disordered regions in protein chain. PLoS Comput. Biol. 2006;2:e177. doi: 10.1371/journal.pcbi.0020177
  8. Galzitskaya OV, Garbuzynskiy SO, Lobanov MYu. FoldUnfold: web server for the prediction of disorderred regions in protein chain. Bioinformatics. 2006;22:2948-2949. doi: 10.1093/bioinformatics/btl504
  9. Galzitskaya OV, Garbuzynskiy SO, Lobanov MYu. Prediction of natively unfolded regions in protein chains. Molecular Biology. 2006;40(2):298-304. doi: 10.1134/S0026893306020166
  10. Coeytaux K, Poupon A. Prediction of unfolded segments in a protein sequence based on amino acid composition. Bioinformatics. 2005;21:1891-1900. doi: 10.1093/bioinformatics/bti266
  11. Dosztányi Z, Csizmók V, Tompa P, Simon I. The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. J. Mol. Biol. 2005;347:827-839.
  12. Dosztányi Z, Csizmók V, Tompa P, Simon I. IUPred: web server for the prediction of intrinsically unstructured regions based on estimated energy content. Bioinformatics. 2005;21:3433-3434. doi: 10.1093/bioinformatics/bti541
  13. Linding R, Russell RB, Neduva V, Gibson TJ. GlobPlot: Exploring protein sequences for globularity and disorder. Nucl. Acids Res. 2003;31:3701-3708. doi: 10.1093/nar/gkg519
  14. Prilusky J, Felder CE, Zeev-Ben-Mordehai T, Rydberg EH, Man O, Beckmann JS, Silman I, Sussman JL. FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics. 2005;21:3435-3438. doi: 10.1093/bioinformatics/bti537
  15. 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. doi: 10.1093/bioinformatics/bti534
  16. Linding R, Jensen L, Diella F, Bork P, Gibson T, Russell R. Protein disorder prediction: implications for structural proteomics. Structure. 2003;11:1453-1459. doi: 10.1016/j.str.2003.10.002
  17. Ward JJ, McGuffin LJ, Bryson K, Buxton BF, Jones DT. The DISOPRED server for the prediction of protein disorder. Bioinformatics. 2004;20:2138-2139. doi: 10.1093/bioinformatics/bth195
  18. Ising E. Beitrag zut Theorie des Ferromagnetizmus. Zeitschr. Phys. 1925;31:253-258. doi: 10.1007/BF02980577
  19. Zimm BH, Bragg JK. Theory of the phase transition between helix and random coil in polypeptide chains. J. Chem. Phys. 1959;31:526-535.
  20. Finkelstein AV. Theory of protein molecule self-organization. III. A calculating method for the probabilities of the secondary structure formation in an unfolded protein chain. Biopolymers. 1977;16:525-529. doi: 10.1002/bip.1977.360160304
  21. Finkelstein AV, Roytberg MA. Computation of biopolymers: A general approach to different problems. BioSystems. 1993;30:1-19. doi: 10.1016/0303-2647(93)90058-K
  22. Melamud E, Moult J. Evaluation of disorder predictions in CASP5. Proteins. 2003;53(6):561-565.
  23. Jin Y, Dunbrack RL, Jr. Assessment of disorder predictions in CASP6. Proteins. 2005;61(7):167-175. doi: 10.1002/prot.20734
  24. Bordoli L, Kiefer F, Schwede T. Assessment of disordered predictions in CASP7. Proteins. 2007;69(8):129-136. doi: 10.1002/prot.21671
  25. Noivirt-Brik O, Prilusky J, Sussman JL. Assessment of disordered predictions in CASP8. Proteins. 2009;77(9):210-216. doi: 10.1002/prot.22586
Table of Contents Original Article
Math. Biol. Bioinf.
2010;5(2):124-137
doi: 10.17537/2010.5.124
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References

 

  Copyright IMPB RAS © 2005-2024