Protein level predictions 5 - Disorder prediction

Disorder prediction is associated with disordered proteins. These kinds of proteins exists and they are important in tasks like molecular recognition, molecular assembly, protein assembly and entropy chain and several other important tasks.  In addition to these proteins mutations may introduce disorder into usually ordered parts of protein and therefore possible change the protein function (Thusberg and Vihinen 2009).

Programs available

• ANCHOR
• CAST
• DisEMBL
• Disopred
• DISpro
• Disprot
• DRIPPRED
• FoldIndex
• FoldUnfold
• GlobPlot
• iPDA
• IUPred
• NORSp
• PONDR
• POODLE
• PrDOS
• PreLink
• RONN
• SEG
• Spritz

An extensive overview of tools predicting protein level changes can be found from the recent review  article by Thusberg and Vihinen.Click here to return to the main page of protein prediction tools.

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Description of programs

ANCHOR

ANCHOR is a web server for predicting protein binding regions in disordered proteins.  Anchor relies on the pairwise energy estimation approach that is the basis for IUPred, a general disorder prediction method. Predictions in ANCHOR combine the general disorder tendency with the sensitivity to the structural environment and it predicts disordered binding regions without any information about the partner protein(s). As minimum input of the web server a single amino acid sequence is needed. Sequences can also be specified by their corresponding UniProt IDs or ACs. A list of motifs can also be submitted, specified as regular expressions with or without their names. Output of ANCHOR is a probability score which indicates the likelihood of the residue to be part of a disordered binding region along each position in the sequence. (Dosztanyi et al).

website: http://anchor.enzim.hu

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Reference: Dosztányi et al. ANCHOR: web server for predicting protein binding regions in disordered proteins. Bioinformatics, 2009, 25, 20, 2745-2746. doi:10.1093/bioinformatics/btp518

CAST

website:

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Reference: Promponas et  al. CAST: an iterative algorithm for the complexity analysis of sequence tracts. Complexity analysis of sequence tracts. Bioinformatics, 2000, 16, 10, 915-922. http://bioinformatics.oxfordjournals.org/cgi/reprint/16/10/915

DisEMBL

website: DisEMBL

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Reference: Linding et al. Protein disorder prediction: implications for structural proteomics. Structure, 2003, 11, 11, 1453-1459. doi:10.1016/j.str.2003.10.002  

Disopred

website: Disopred

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Reference: Ward et al. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J.Mol.Biol., 2004, 337, 3, 635-645. doi:10.1016/j.jmb.2004.02.002   

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DISpro

website: Dispro

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Reference: Cheng et al. SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res., 2005, 33, Web Server issue, W72-6. doi:10.1093/nar/gki396

Disprot

website: Disprot

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References:

• Obradovic et al. Predicting intrinsic disorder from amino acid sequence. Proteins, 2003, 53 Suppl 6, 566-572. doi:10.1002/prot.10532

• Peng et al. Optimizing long intrinsic disorder predictors with protein evolutionary information. J.Bioinform Comput.Biol., 2005, 3, 1, 35-60. DOI: 10.1142/S0219720005000886

• Vucetic et al. Flavors of protein disorder. Proteins, 2003, 52, 4, 573-584. doi:10.1002/prot.10437

DRIPPRED

website: DRIPPRED

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Reference:

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FoldIndex

website: FoldIndex

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Reference: Prilusky et al. FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics, 2005, 21, 16, 3435-3438. doi:10.1093/bioinformatics/bti537

FoldUnfold

website: FoldUnfold

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Reference: Galzitskaya et al. FoldUnfold: web server for the prediction of disordered regions in protein chain. Bioinformatics, 2006, 22, 23, 2948-2949. doi:10.1093/bioinformatics/btl504

GlobPlot

website: GlobPlot

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Reference: Linding et al. GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res., 2003, 31, 13, 3701-3708.

doi:10.1093/nar/gkg519

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iPDA

website: iPDA

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Reference: Su et al. iPDA: integrated protein disorder analyzer. Nucleic Acids Res., 2007, 35, Web Server issue, W465-72. doi:10.1093/nar/gkm353

IUPred

website: IUPred

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Reference: Dosztanyi et al. IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics, 2005, 21, 16, 3433-3434. doi:10.1093/bioinformatics/bti541

NORSp

website: NORSp

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Reference: Liu and Rost. NORSp: Predictions of long regions without regular secondary structure. Nucleic Acids Res., 2003, 31, 13, 3833-3835. doi:10.1093/nar/gkg515

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PONDR

website: PONDR

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Reference:

• Obradovic et al. Exploiting heterogeneous sequence properties improves prediction of protein disorder. Proteins, 2005, 61 Suppl 7, 176-182. doi:10.1002/prot.20735

• Romero et al. Sequence complexity of disordered protein. Proteins, 2001, 42, 1, 38-48. doi:10.1002/1097-0134(20010101)42:1<38::AID-PROT50>3.0.CO;2-3
  

POODLE

website: POODLE

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Reference:

• Hirose et al. POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions. Bioinformatics, 2007, 23, 16, 2046-2053. doi:10.1093/bioinformatics/btm302

• Shimizu et al. POODLE-S: web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix. Bioinformatics, 2007, 23, 17, 2337-2338. doi:10.1093/bioinformatics/btm330

PrDOS

website: PrDOS

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Reference: Ishida and Kinoshita. PrDOS: prediction of disordered protein regions from amino acid sequence. Nucleic Acids Res., 2007, 35, Web Server issue, W460-4. doi:10.1093/nar/gkm363

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PreLink

website: PreLink

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Reference: Coeytaux and Puopon. Prediction of unfolded segments in a protein sequence based on amino acid composition. Bioinformatics, 2005, 21, 9, 1891-1900.doi:10.1093/bioinformatics/bti266

RONN

website: RONN

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Reference: Yang et al. RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics, 2005, 21, 16, 3369-3376. doi:10.1093/bioinformatics/bti534

SEG

website: SEG

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Reference: Wootton. Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput.Chem., 1994, 18, 3, 269-285. doi:10.1016/0097-8485(94)85023-2  

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Spritz

website: Spritz

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Reference: Vullo et al. Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines. Nucleic Acids Res., 2006, 34, Web Server issue, W164-8. doi: 10.1093/nar/gkl166.

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Useful databases

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Review articles

• Janita Thusberg and Mauno Vihinen. Pathogenic or Not? And If So, Then How? Studying the Effects of Missense Mutations Using Bioinformatics Methods. Hum Mutat. 2009 May;30(5):703-14: doi:10.1002/humu.20938

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Other articles

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Useful Links

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