IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content

By Zsuzsanna Dosztányi, Veronika Csizmok, Peter Tompa, István Simon. 2005

2,006 citations recorded by the source corpus.

Subfields: Molecular Biology, Spectroscopy

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Citations in the corpus

SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning (2019, methodology): “JRONN [67], IUPred optimized for short and long disorder [IUpred (short)] and [IUpred (long)] [15], and PONDR-VSL [14] are not discussed here because of lower performance except the second-best shown below.”
IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding (2018, methodology): “These options are directly inherited from the previous IUPred implementation (19,25).”
RaptorX-Property: a web server for protein structure property prediction (2016, neutral): “For DISO, we compare with IUpred (27) and Diso-Pred3 (28).”
Understanding eukaryotic linear motifs and their role in cell signaling and regulation. (2008, background): “IUPred intrinsically captures physico-chemical information in its algorithm (111).”
Intrinsically disordered proteins in human diseases: introducing the D2 concept. (2008, methodology): “These compositional differences were used to develop numerous disorder predictors, including PONDR ©R (predictor of naturally disordered regions) (113), charge-hydropathy plots (CH-plots) (139), and IUPred (34), to name a few.”
G3BP–Caprin1–USP10 complexes mediate stress granule condensation and associate with 40S subunits (2016, methodology): “ID regions were determined using the programs of Dosztányi et al. (2005) on the ANC HOR website (http :// anchor .enzim .hu /), in which regions of disorder >50% on the intrinsically unordered histograms were graphically rendered (red) for simplicity.”
MODBASE: a database of annotated comparative protein structure models and associated resources (2005, background): “The sequences of our previous analysis were further annotated by fraction of predicted disordered regions (70,71), number of glycosylation sites (2,72,73), clone availability (74–76), HUGO annotations (77), sequence length and several additional metrics.”
p53 Proteoforms and Intrinsic Disorder: An Illustration of the Protein Structure–Function Continuum Concept (2016, methodology): “pro/) [113], which represents the outputs of IUPred [114], PONDR® VLXT [115], PrDOS [116], PONDR® VSL2B [117,118], PV2 [113], and ESpritz [119].”
A decade and a half of protein intrinsic disorder: Biology still waits for physics (2013, background): “1, [11] [12] [13] [14] 31, 73, 78, 79, 132, 134, [138] [139] [140] 142, 144, 153 Functions of many IDPs/IDPRs rely on interactions with specific binding partners, and many IDPs/IDPRs tend to undergo disorder-to-order transitions as a result of binding to their specific targets.”
Prediction of Protein Binding Regions in Disordered Proteins (2009, methodology): “This problem was addressed by calculating the fraction of amino acids that are predicted as binding sites in general disordered regions of Disprot database that are correctly recognized as disordered by IUPred.”