iupred: Prediction of Intrinsic Disorder with IUPred2A

In idpr: Profiling and Analyzing Intrinsically Disordered Proteins in R

Description

This function makes a connection to the IUPred2A REST API based on the type of analysis and UniProt accession number. This requires the user to know the accession number of their protein and a connection to the internet. The results are then formatted to match output in the idpr package.

Predictions are made on a scale of 0-1, where any residues with a score over 0.5 are predicted to be disordered, and any residue scoring below 0.5 are predicted to be ordered (when using "long" and "short" predictions).
The output is either a graph (ggplot) or data frame of predictions.

iupred() is used for standard predictions of intrinsic disorder of an amino acid sequence. This is the core of predictions. Predictions vary by iupredType (details below) The results are either a ggplot or data frame of the fetched IUPred2. predictions.
iupredAnchor() is used to combine the output of IUPred2 long with ANCHOR2 predictions. ANCHOR2 is a context-dependent predictor of binding regions for protein-protein interactions. The results are either a ggplot with 2 lines, one for IUPred2 long and another for ANCHOR predictions, or a data frame with both IUPred2 long and ANCHOR Predictions. Values are fetched by the IUPred2A REST API.
iupredRedox() is used to predict redox-sensitive regions that may experience induced folding upon changing environments. This is a context-dependent predictor of disordered regions depending on a reducing (plus) or oxidizing (minus) environment. The results can be a ggplot with two IUPred2 long predictions, one for plus and another for minus environments, with redox sensitive regions shaded (if predicted). Alternatively, the results can be a data frame with both IUPred2 long plus and minus predictions as well as a column of logical values where a residue that is TRUE is predicted to be in a redox sensitive region. Values are fetched by the IUPred2A REST API.

IUPred2 website is located at https://iupred2a.elte.hu/. For detailed information on using IUPred2A, please refer to Erdős & Dosztány (2020) Analyzing protein disorder with IUPred2A. Current Protocols in Bioinformatics, 70, e99. Additionally, please see Mészáros et al (2019) for further information, theory, and applications of IUPred2A.

Please cite these articles if you use any iupred function.

Usage

iupred(
  uniprotAccession,
  iupredType = "long",
  plotResults = TRUE,
  proteinName = NA
)

iupredAnchor(uniprotAccession, plotResults = TRUE, proteinName = NA)

iupredRedox(uniprotAccession, plotResults = TRUE, proteinName = NA)

Arguments

uniprotAccession	character string specifying the UniProt Accession of the protein of interest. Used to fetch predictions from IUPreds REST API
iupredType	character string. "long" by default. accepted types are c("long", "short", "glob"). See "Prediction Type" information below.
plotResults	logical value. TRUE by default. If plotResults = TRUE, a ggplot of IUPred predictions is returned If plotResults = FALSE, a data frame of predictions is returned.
proteinName	character string, optional. Used to add protein name to the title in ggplot. Ignored if plotResults = FALSE.

Value

see plotResults argument.

Prediction Type

Information from https://iupred2a.elte.hu/help_new on 5.22.20 Additionally, see the sources for further details and source information. This is only relevant for iupred(). iupredAnchor() and iupredRedox() always utilize "long" for data in the REST API.

• Long predictions of disorder (Default)

  • when iupredType = "long"

  • Optimized for global predictions of disorder, specifically disordered regions over 30 amino acids in length.

  • "long" is always used for iupredAnchor() and iupredRedox().

• Short predictions of disorder

  • when iupredType = "short"

  • Best for predicting small regions of disorder, especially in mostly structured proteins.

  • Has adjustments for termini, since sequence ends are often disordered.

• Structured predictions

  • when iupredType = "glob"

  • Used to predict regions of globular folding.

  • please see Erdős & Dosztány (2020) for further information on interpreting these results.

Plot Colors

For users who wish to keep a common aesthetic, the following colors are used when plotResults = TRUE.

• iupred() iupredType = 'long', 'short', or 'glob'. Additionally, the 'long' prediction with iupredAnchor().

  • Dynamic iupred line colors:

    • Close to 0 = "darkolivegreen3" or "#A2CD5A"

    • Close to 1 = "darkorchid1" or "#BF3EFF"

    • Close to 0.5 (midpoint) = "grey65" or "#A6A6A6"

• iupredAnchor :

  • Solid Line (ANCHOR2 Score) = "#92140C"

• iupredRedox:

  • iupredPlus line = "darkorchid1" or "#BF3EFF"

  • iupredMin line = "#348AA7"

  • redox sensitive regions = "#5DD39E"

Source

Bálint Mészáros, Gábor Erdős, Zsuzsanna Dosztányi, IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding, Nucleic Acids Research, Volume 46, Issue W1, 2 July 2018, Pages W329–W337, https://doi.org/10.1093/nar/gky384

Erdős, G., & Dosztányi, Z. (2020). Analyzing protein disorder with IUPred2A. Current Protocols in Bioinformatics, 70, e99. https://doi.org/10.1002/cpbi.99

Examples

#A UniProt Accession must be specified.
##this example uses human P53.
TP53_UniProt <- "P04637"
## Not run: 
#Getting data as a data frame
exampleDF_long <- iupred(uniprotAccession = TP53_UniProt,
                         iupredType = "long",
                         plotResults = FALSE)
head(exampleDF_long)

exampleDF_short <- iupred(uniprotAccession = TP53_UniProt,
                          iupredType = "short",
                          plotResults = FALSE)
head(exampleDF_short)

exampleDF_anchor <- iupredAnchor(uniprotAccession = TP53_UniProt,
                                 plotResults = FALSE)
head(exampleDF_anchor)

exampleDF_redox <- iupredRedox(uniprotAccession = TP53_UniProt,
                              plotResults = FALSE)
head(exampleDF_redox)

#Plotting

iupred(uniprotAccession = TP53_UniProt,
    iupredType = "long",
    plotResults = TRUE)

iupred(uniprotAccession = TP53_UniProt,
    iupredType = "short",
    plotResults = TRUE)

iupredAnchor(uniprotAccession = TP53_UniProt,
          plotResults = TRUE)

iupredRedox(uniprotAccession = TP53_UniProt,
         plotResults = TRUE)

## End(Not run)
#A valid internet connection is needed to make
##A connection with the IUPred REST API

idpr documentation built on Dec. 26, 2020, 6 p.m.