List of methods for prediction of intrinsically unstructured proteins
Method overview
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Paper about "MetaDisorder"
Gallery of IUPs
List of protein disorder predictors

List of programs for predicition of intrinsically unstructured proteins (protein disorder)

As of October 2012, over 60 methods for computational prediction of protein disorder from sequence have been made publicly available. Here, we report ~ 40 methods, which we have tested (it means that we were able to run them and they returned protein disorder prediction). Methods which are no longer available (url is dead, servers did not respond, etc.) are in grey. Note, that some of programs are presented here as one method, while actually they are can be viewed as two or more different versions (eg. POODLE-L, POODLE-S, IUPred with long and short option, etc.).

You can run by one click over 10 listed below methods by running our metaDisorder Predictor (Submit sequence)

Dosztqanyi Z, Meszaros B, Simon I. ANCHOR: web server for predicting protein binding regions in disordered proteins. Bioinformatics. 2009 Oct 15;25(20):2745-6. Epub 2009 Aug 28. PubMed PMID: 19717576; PubMed Central PMCID: PMC2759549.
Walsh I, Martin AJ, Di Domenico T, Vullo A, Pollastri G, Tosatto SC. CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W190-6. Epub 2011 Jun 6. PubMed PMID: 21646342; PubMed Central PMCID: PMC3125791.
Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB. Protein disorder prediction: implications for structural proteomics. Structure. 2003 Nov;11(11):1453-9. PubMed PMID: 14604535.
McGuffin LJ. Intrinsic disorder prediction from the analysis of multiple protein fold recognition models. Bioinformatics. 2008 Aug 15;24(16):1798-804. Epub 2008 Jun 25. PubMed PMID: 18579567.
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 Mar 26;337(3):635-45. PubMed PMID: 15019783.

Vucetic S, Brown CJ, Dunker AK, Obradovic Z. Flavors of protein disorder. Proteins. 2003 Sep 1;52(4):573-84. PubMed PMID: 12910457.
replaced by iPDA
Su CT, Chen CY, Ou YY. Protein disorder prediction by condensed PSSM considering propensity for order or disorder. BMC Bioinformatics. 2006 Jun 23;7:319. PubMed PMID: 16796745; PubMed Central PMCID: PMC1526762.
No publication
Baldi P, Pollastri G. The principled design of large-scale recursive neural network architectures dag rnns and the protein structure prediction problem. J. Mach. Learn. 2003;4:575-602.
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 Aug 15;21(16):3435-8. Epub 2005 Jun 14. PubMed PMID: 15955783.
Galzitskaya OV, Garbuzynskiy SO, Lobanov MY. FoldUnfold: web server for the prediction of disordered regions in protein chain. Bioinformatics. 2006 Dec 1;22(23):2948-9. Epub 2006 Oct 4. PubMed PMID: 17021161.
Kozlowski LP, Bujnicki JM. MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins. BMC Bioinformatics. 2012 May 24;13:111. doi: 10.1186/1471-2105-13-111. PubMed PMID: 22624656; PubMed Central PMCID: PMC3465245.
GeneSilico MetaDisorder
Linding R, Russell RB, Neduva V, Gibson TJ. GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res. 2003 Jul 1;31(13):3701-8. PubMed PMID: 12824398; PubMed Central PMCID: PMC169197.
Holladay NB, Kinch LN, Grishin NV. Optimization of linear disorder predictors yields tight association between crystallographic disorder and hydrophobicity. Protein Sci. 2007 Oct;16(10):2140-52. PubMed PMID: 17893360; PubMed Central PMCID: PMC2204125.
Grishin Lab Disorder Predictor
Su CT, Chen CY, Hsu CM. iPDA: integrated protein disorder analyzer. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W465-72. Epub 2007 Jun 6. PubMed PMID: 17553839; PubMed Central PMCID: PMC1933224.
iPDA, mirror
Han P, Zhang X, Norton RS, Feng ZP. Large-scale prediction of long disordered regions in proteins using random forests. BMC Bioinformatics. 2009 Jan 7;10:8. PubMed PMID: 19128505; PubMed Central PMCID: PMC2637845.
Dosztanyi Z, Csizmok V, Tompa P, Simon I. IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics. 2005 Aug 15;21(16):3433-4. Epub 2005 Jun 14. PubMed PMID: 15955779.
Lieutaud P, Canard B, Longhi S. MeDor: a metaserver for predicting protein disorder. BMC Genomics. 2008 Sep 16;9 Suppl 2:S25. PubMed PMID: 18831791; PubMed Central PMCID: PMC2559890.
Ishida T, Kinoshita K. Prediction of disordered regions in proteins based on the meta approach. Bioinformatics. 2008 Jun 1;24(11):1344-8. Epub 2008 Apr 20. PubMed PMID: 18426805.
Mizianty MJ, Stach W, Chen K, Kedarisetti KD, Disfani FM, Kurgan L. Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources. Bioinformatics. 2010 Sep 15;26(18):i489-96. PubMed PMID: 20823312; PubMed Central PMCID: PMC2935446.
Disfani FM, Hsu WL, Mizianty MJ, Oldfield CJ, Xue B, Dunker AK, Uversky VN, Kurgan L. MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins. Bioinformatics. 2012 Jun 15;28(12):i75-83. PubMed PMID: 22689782; PubMed Central PMCID: PMC3371841.
Liu J, Rost B. NORSp: Predictions of long regions without regular secondary structure. Nucleic Acids Res. 2003 Jul 1;31(13):3833-5. PubMed PMID: 12824431; PubMed Central PMCID: PMC168922.
Wang L, Sauer UH. OnD-CRF: predicting order and disorder in proteins using [corrected] conditional random fields. Bioinformatics. 2008 Jun 1;24(11):1401-2. Epub 2008 Apr 21. Erratum in: Bioinformatics. 2008 Jul 1;24(13):1562. PubMed PMID: 18430742; PubMed Central PMCID: PMC2387219.
No paper
Romero P, Obradovic Z, Li X, Garner EC, Brown CJ, Dunker AK. Sequence complexity of disordered protein. Proteins. 2001 Jan 1;42(1):38-48. PubMed PMID: 11093259
Xue B, Dunbrack RL, Williams RW, Dunker AK, Uversky VN. PONDR-FIT: a meta-predictor of intrinsically disordered amino acids. Biochim Biophys Acta. 2010 Apr;1804(4):996-1010. Epub 2010 Jan 25. PubMed PMID: 20100603; PubMed Central PMCID: PMC2882806.
Hirose S, Shimizu K, Kanai S, Kuroda Y, Noguchi T. POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions. Bioinformatics. 2007 Aug 15;23(16):2046-53. Epub 2007 Jun 1. PubMed PMID: 17545177.
Ishida T, Kinoshita K. PrDOS: prediction of disordered protein regions from amino acid sequence. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W460-4. Epub 2007 Jun 12. PubMed PMID: 17567614; PubMed Central PMCID: PMC1933209.
Deng X, Eickholt J, Cheng J. PreDisorder: ab initio sequence-based prediction of protein disordered regions. BMC Bioinformatics. 2009 Dec 21;10:436. PubMed PMID: 20025768; PubMed Central PMCID: PMC3087350.
Quevillon-Cheruel S, Leulliot N, Gentils L, van Tilbeurgh H, Poupon A. Production and crystallization of protein domains: how useful are disorder predictions ? Curr Protein Pept Sci. 2007 Apr;8(2):151-60. Review. PubMed PMID: 17430196.
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 Aug 15;21(16):3369-76. Epub 2005 Jun 9. PubMed PMID: 15947016.
Schlessinger A, Punta M, Yachdav G, Kajan L, Rost B. Improved disorder prediction by combination of orthogonal approaches. PLoS One. 2009;4(2):e4433. Epub 2009 Feb 11. PubMed PMID: 19209228; PubMed Central PMCID: PMC2635965.
Rost Metadisorder
Wootton JC. Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput Chem. 1994 Sep;18(3):269-85. PubMed PMID: 7952898.
Zhang T, Faraggi E, Xue B, Dunker AK, Uversky VN, Zhou Y. SPINE-D: accurate prediction of short and long disordered regions by a single neural-network based method. J Biomol Struct Dyn. 2012;29(4):799-813. PubMed PMID: 22208280; PubMed Central PMCID: PMC3297974.
Vullo A, Bortolami O, Pollastri G, Tosatto SC. Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W164-8. PubMed PMID: 16844983; PubMed Central PMCID: PMC1538873.
Schlessinger A, Punta M, Rost B. Natively unstructured regions in proteins identified from contact predictions. Bioinformatics. 2007 Sep 15;23(18):2376-84. Epub 2007 Aug 20. PubMed PMID: 17709338.
Contact: Lukasz Kozlowski

If you find this site useful, please consider citing the reference:
Kozlowski LP, Bujnicki JM. MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins. BMC Bioinformatics. 2012 May 24;13(1):111.

This work was supported by Polish Ministry of Science and Higher Education (grant NN301 190139).

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