foldIndexR: Prediction of Intrinsic Disorder with FoldIndex method in R

In wmm27/idpr: Profiling and Analyzing Intrinsically Disordered Proteins in R

Prediction of Intrinsic Disorder with FoldIndex method in R

Description

This is used to calculate the prediction of intrinsic disorder based on the scaled hydropathy and absolute net charge of an amino acid sequence using a sliding window. FoldIndex described this relationship and implemented it graphically in 2005 by Prilusky, Felder, et al, and this tool has been implemented into multiple disorder prediction programs. When windows have a negative score (<0) sequences are predicted as disordered. When windows have a positive score (>0) sequences are predicted as disordered. Graphically, this cutoff is displayed by the dashed line at y = 0. Calculations are at pH 7.0 based on the described method and the default is a sliding window of size 51.

Usage

foldIndexR(
  sequence,
  window = 51,
  proteinName = NA,
  pKaSet = "IPC_protein",
  plotResults = TRUE,
  ...
)

Arguments

sequence	amino acid sequence as a single character string, a vector of single characters, or an AAString object. It also supports a single character string that specifies the path to a .fasta or .fa file.
window	a positive, odd integer. 51 by default. Sets the size of sliding window, must be an odd number. The window determines the number of residues to be analyzed and averaged for each position along the sequence.
proteinName	character string with length = 1. optional setting to replace the name of the plot if plotResults = TRUE.
pKaSet	A character string or data frame. "IPC_protein" by default. Character string to load specific, preloaded pKa sets. c("EMBOSS", "DTASelect", "Solomons", "Sillero", "Rodwell", "Lehninger", "Toseland", "Thurlkill", "Nozaki", "Dawson", "Bjellqvist", "ProMoST", "Vollhardt", "IPC_protein", "IPC_peptide") Alternatively, the user may supply a custom pKa dataset. The format must be a data frame where: Column 1 must be a character vector of residues named "AA" AND Column 2 must be a numeric vector of pKa values.
plotResults	logical value, TRUE by default. If plotResults = TRUE a plot will be the output. If plotResults = FALSE the output is a data frame with scores for each window analyzed.
...	any additional parameters, especially those for plotting.

Details

The output is either a data frame or graph showing the calculated scores for each window along the sequence. The equation used was originally described in Uversky et al. (2000)
https://doi.org/10.1002/1097-0134(20001115)41:3<415::AID-PROT130>3.0.CO;2-7 .
The FoldIndex method of using a sliding window and utilizing the Uversky equation is described in Prilusky, J., Felder, C. E., et al. (2005).
FoldIndex: a simple tool to predict whether a given protein sequence
is intrinsically unfolded. Bioinformatics, 21(16), 3435-3438.

Value

see plotResults argument

Plot Colors

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

• Dynamic line colors:

  • Close to -1 = "#9672E6"

  • Close to 1 = "#D1A63F"

  • Close to midpoint = "grey65" or "#A6A6A6"

References

Kyte, J., & Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. Journal of molecular biology, 157(1), 105-132. Kozlowski, L. P. (2016). IPC – Isoelectric Point Calculator. Biology Direct, 11(1), 55. https://doi.org/10.1186/s13062-016-0159-9
Kyte, J., & Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. Journal of molecular biology, 157(1), 105-132.
Prilusky, J., Felder, C. E., et al. (2005).
FoldIndex: a simple tool to predict whether a given protein sequence
is intrinsically unfolded. Bioinformatics, 21(16), 3435-3438.
Uversky, V. N., Gillespie, J. R., & Fink, A. L. (2000). Why are “natively unfolded” proteins unstructured under physiologic conditions?. Proteins: structure, function, and bioinformatics, 41(3), 415-427. https://doi.org/10.1002/1097-0134(20001115)41:3<415::AID-PROT130>3.0.CO;2-7

See Also

KDNorm for residue hydropathy values. See pKaData for residue pKa values and citations. See hendersonHasselbalch for charge calculations.

Other scaled hydropathy functions: KDNorm, meanScaledHydropathy(), scaledHydropathyGlobal(), scaledHydropathyLocal()

wmm27/idpr documentation built on Jan. 12, 2023, 8:45 a.m.