@@ -1,7 +1,7 @@

 Package: idpr

 Type: Package

 Title: Profiling and Analyzing Intrinsically Disordered Proteins in R

-Version: 1.0.007

+Version: 1.6.1

 Authors@R: c(person(c("William", "M."), "McFadden", 

                 email = "wmm27@pitt.edu", 

                 role = c("cre", "aut")),

@@ -23,9 +23,9 @@ License: LGPL-3

 Encoding: UTF-8

 LazyData: true

 biocViews: StructuralPrediction, Proteomics, CellBiology

-RoxygenNote: 7.1.1

+RoxygenNote: 7.1.2

 Depends: 

-    R (>= 4.0.0)

+    R (>= 4.1.3)

 Imports: 

     ggplot2 (>= 3.3.0),

     magrittr (>= 1.5),

@@ -3,6 +3,7 @@

 export(chargeCalculationGlobal)

 export(chargeCalculationLocal)

 export(chargeHydropathyPlot)

+export(foldIndexR)

 export(hendersonHasselbalch)

 export(idprofile)

 export(iupred)

new file mode 100644

@@ -0,0 +1,131 @@

+#' Prediction of Intrinsic Disorder with FoldIndex method in R

+#'

+#' 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. 

+#'   

+#'   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)\cr

+#'   \url{https://doi.org/10.1002/1097-0134(20001115)41:3<415::AID-PROT130>3.0.CO;2-7}

+#'   . \cr

+#'   

+#'   The FoldIndex method of using a sliding window and utilizing the uversky 

+#'   equation is described in Prilusky, J., Felder, C. E., et al. (2005). \cr

+#'   FoldIndex: a simple tool to predict whether a given protein sequence \cr 

+#'   is intrinsically unfolded. Bioinformatics, 21(16), 3435-3438. \cr

+#'   

+#'   

+#' @inheritParams sequenceCheck

+#' @inheritParams chargeCalculationLocal

+#' @param 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.

+#' @param plotResults logical value, TRUE by default.

+#'   If \code{plotResults = TRUE} a plot will be the output.

+#'   If \code{plotResults = FALSE} the output is a data frame with scores for

+#'   each window analyzed.

+#' @param proteinName character string with length = 1.

+#'   optional setting to replace the name of the plot if plotResults = TRUE.

+#' @param ... any additional parameters, especially those for plotting.

+#' @return see plotResults argument

+#' @family scaled hydropathy functions

+#' @seealso \code{\link{KDNorm}} for residue hydropathy values.

+#'   See \code{\link{pKaData}} for residue pKa values and citations. See

+#'   \code{\link{hendersonHasselbalch}} for charge calculations.

+#' @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.

+#' @export

+#' @section Plot Colors:

+#'   For users who wish to keep a common aesthetic, the following colors are

+#'   used when plotResults = TRUE. \cr

+#'   \itemize{

+#'   \item Dynamic line colors: \itemize{

+#'   \item Close to -1 = "#9672E6"

+#'   \item Close to 1 = "#D1A63F"

+#'   \item Close to midpoint = "grey65" or "#A6A6A6"}}

+#'    

+#'   @references

+#'   Kozlowski, L. P. (2016). IPC – Isoelectric Point Calculator. Biology

+#'   Direct, 11(1), 55. \url{https://doi.org/10.1186/s13062-016-0159-9} \cr

+#'   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. \cr

+#'   Prilusky, J., Felder, C. E., et al. (2005). \cr

+#'   FoldIndex: a simple tool to predict whether a given protein sequence \cr 

+#'   is intrinsically unfolded. Bioinformatics, 21(16), 3435-3438. \cr

+#'   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.

+#'   \url{https://doi.org/10.1002/1097-0134(20001115)41:3<415::AID-PROT130>3.0.CO;2-7}

+#' @examples

+#' #Amino acid sequences can be character strings

+#' aaString <- "ACDEFGHIKLMNPQRSTVWY"

+#' #Amino acid sequences can also be character vectors

+#' aaVector <- c("A", "C", "D", "E", "F",

+#'               "G", "H", "I", "K", "L",

+#'               "M", "N", "P", "Q", "R",

+#'               "S", "T", "V", "W", "Y")

+#' #Alternatively, .fasta files can also be used by providing

+#'   ##The path to the file as a character string.

+#'

+#'

+#' foldIndexR(aaVector)

+#'

+#' exampleDF <- 

+#'   foldIndexR(aaString,

+#'       plotResults = FALSE)

+#' head(exampleDF)

+#' 

+

+foldIndexR <- function(sequence,

+                       window = 51, 

+                       proteinName = NA,

+                       pKaSet = "IPC_protein",

+                       plotResults = TRUE) {

+    

+    chargeDF <-

+        chargeCalculationLocal(sequence = sequence, window = window,

+                               pH = 7.0, pKaSet = pKaSet, 

+                               plotResults = FALSE)

+    chargeDF$scaledWindowCharge <- chargeDF$windowCharge / window

+    hydropDF <-  scaledHydropathyLocal(sequence = sequence, 

+                                       window = window,

+                                       plotResults = FALSE)

+    mergeDF <- merge(hydropDF, chargeDF)

+    

+    mergeDF$foldIndex <- 

+        mergeDF$WindowHydropathy * 2.785 - 

+        abs(mergeDF$scaledWindowCharge) - 1.151

+    

+    if (plotResults) {

+        plotTitle <- "FoldIndex Prediction of Intrinsic Disorder"

+        if (!is.na(proteinName)) {

+            plotTitle <- 

+                paste0("FoldIndex Prediction of Intrinsic Disorder in ", 

+                       proteinName, sep = "")

+        }

+        

+        gg <-  sequencePlot(position = mergeDF$Position,

+                            property = mergeDF$foldIndex,

+                            hline = 0, dynamicColor = mergeDF$foldIndex,

+                            customColors = c("#9672E6", "#D1A63F", "grey65"),

+                            customTitle = NA, propertyLimits = c(-1, 1))

+        gg <- gg + ggplot2::labs(title = plotTitle, y = "Score")

+        return(gg)

+    } else {

+        return(mergeDF)

+    }

+    

+}

@@ -7,6 +7,7 @@

 #'   \code{\link{chargeCalculationLocal}}\cr

 #'   \code{\link{scaledHydropathyLocal}}\cr

 #'   \code{\link{structuralTendencyPlot}}\cr

+#'   \code{\link{foldIndexR}}\cr

 #'   All of the above linked functions only require the sequence argument

 #'   to output plots of characteristics associated with IDPs. The function also

 #'   includes options for IUPred functions. The function does one of the

@@ -24,7 +25,11 @@

 #' @param uniprotAccession character string specifying the UniProt Accession of

 #'   the protein of interest. Used to fetch predictions from IUPreds REST API.

 #'   Default is NA. Keep as NA if you do not have a UniProt Accession.

-#'

+#' @param 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. 51 is default for 

+#'   \code{\link{foldIndexR}}\cr.

 #' @param proteinName character string, optional.

 #'   Used to add protein name to the title in ggplot.

 #' @inheritParams chargeCalculationLocal

@@ -66,6 +71,7 @@

 #'   \code{\link{chargeCalculationLocal}}\cr

 #'   \code{\link{scaledHydropathyLocal}}\cr

 #'   \code{\link{structuralTendencyPlot}}\cr

+#'   \code{\link{foldIndexR}}\cr

 #'   \code{\link{iupred}}\cr

 #'   \code{\link{iupredAnchor}}\cr

 #'   \code{\link{iupredRedox}}

@@ -112,6 +118,19 @@

 #'               Protein Science, 22(6), 693-724.

 #'               doi:10.1002/pro.2261 }

 #'     }

+#'     \item \code{\link{foldIndexR}}

+#'       \itemize{

+#'         \item{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.}

+#'          \item{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}

+#'         \item{Also see citations for hydrapthy and charge plots above}

+#'     }

 #'     \item \code{\link{iupred}},

 #'           \code{\link{iupredAnchor}},

 #'           \code{\link{iupredRedox}}

@@ -155,7 +174,7 @@ idprofile <- function(

     uniprotAccession = NA,

     proteinName = NA,

     iupredType = "long",

-    window = 9,

+    window = 51,

     pH = 7.2,

     pKaSet = "IPC_protein",

     structuralTendencyType = "bar",

@@ -180,6 +199,12 @@ idprofile <- function(

         plotResults = TRUE,

         pKaSet = pKaSet,

         proteinName = proteinName)

+    hydropPlot <- scaledHydropathyLocal(

+        sequence = sequence,

+        window = window,

+        plotResults = TRUE,

+        pKaSet = pKaSet,

+        proteinName = proteinName)

     tendencyPlot <- structuralTendencyPlot(

         sequence = sequence,

         graphType = structuralTendencyType,

@@ -188,6 +213,10 @@ idprofile <- function(

         disorderNeutral = disorderNeutral,

         orderPromoting = orderPromoting,

         proteinName = proteinName)

+    foldIndexPlot <- foldIndexR(sequence = sequence,

+        window = window, 

+        proteinName = proteinName,

+        pKaSet = pKaSet) 

     #-------- Adding IUPred Plot based on which type

     if (!is.na(uniprotAccession)) {

@@ -216,6 +245,7 @@ idprofile <- function(

                 label = "No Uniprot Accession provided...IUPred plot skipped") +

             ggplot2::theme_void()

     }

-    plotList <- list(rhPlot, tendencyPlot, chargePlot, hydropPlot, iupredPlot)

+    plotList <- list(rhPlot, tendencyPlot, chargePlot, hydropPlot, 

+                     foldIndexPlot, iupredPlot)

     return(plotList)

 }

@@ -85,7 +85,7 @@ idprofile(sequence = P53_HUMAN, #Generates the Profile

 **idpr package.**

 [Link to the Vignette (here)](https://bioconductor.org/packages/release/bioc/vignettes/idpr/inst/doc/idpr-vignette.html)

-

+ 

 ## Appendix

 ### Package citation

@@ -89,6 +89,11 @@ idprofile(sequence = P53_HUMAN, #Generates the Profile

 <img src="man/figures/README-example-5.png" width="75%" />

+    #> 

+    #> [[6]]

+

+<img src="man/figures/README-example-6.png" width="75%" />

+

 **Please Refer to idpr-vignette.Rmd file for a detailed introduction to

 the** **idpr package.** [Link to the Vignette

 (here)](https://bioconductor.org/packages/release/bioc/vignettes/idpr/inst/doc/idpr-vignette.html)

@@ -104,7 +109,7 @@ citation("idpr")

 #> 

 #>   William M. McFadden and Judith L. Yanowitz (2020). idpr: Profiling

 #>   and Analyzing Intrinsically Disordered Proteins in R. R package

-#>   version 1.0.005.

+#>   version 1.6.1.

 #> 

 #> A BibTeX entry for LaTeX users is

 #> 

@@ -112,7 +117,7 @@ citation("idpr")

 #>     title = {idpr: Profiling and Analyzing Intrinsically Disordered Proteins in R},

 #>     author = {William M. McFadden and Judith L. Yanowitz},

 #>     year = {2020},

-#>     note = {R package version 1.0.005},

+#>     note = {R package version 1.6.1},

 #>   }

 ```

@@ -120,9 +125,9 @@ citation("idpr")

 ``` r

 Sys.time()

-#> [1] "2020-12-23 14:07:28 EST"

+#> [1] "2022-03-11 02:31:26 EST"

 Sys.Date()

-#> [1] "2020-12-23"

+#> [1] "2022-03-11"

 R.version

 #>                _                           

 #> platform       x86_64-apple-darwin17.0     

@@ -131,12 +136,12 @@ R.version

 #> system         x86_64, darwin17.0          

 #> status                                     

 #> major          4                           

-#> minor          0.3                         

-#> year           2020                        

-#> month          10                          

+#> minor          1.3                         

+#> year           2022                        

+#> month          03                          

 #> day            10                          

-#> svn rev        79318                       

+#> svn rev        81868                       

 #> language       R                           

-#> version.string R version 4.0.3 (2020-10-10)

-#> nickname       Bunny-Wunnies Freak Out

+#> version.string R version 4.1.3 (2022-03-10)

+#> nickname       One Push-Up

 ```

@@ -28,6 +28,7 @@ A dataset containing a measure of hydropathy for each amino acid residue

 }

 \seealso{

 Other scaled hydropathy functions: 

+\code{\link{foldIndexR}()},

 \code{\link{meanScaledHydropathy}()},

 \code{\link{scaledHydropathyGlobal}()},

 \code{\link{scaledHydropathyLocal}()}

Binary files a/man/figures/README-example-3.png and b/man/figures/README-example-3.png differ

Binary files a/man/figures/README-example-4.png and b/man/figures/README-example-4.png differ

Binary files a/man/figures/README-example-5.png and b/man/figures/README-example-5.png differ

new file mode 100644

Binary files /dev/null and b/man/figures/README-example-6.png differ

new file mode 100644

@@ -0,0 +1,135 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/foldIndexR.R

+\name{foldIndexR}

+\alias{foldIndexR}

+\title{Prediction of Intrinsic Disorder with FoldIndex method in R}

+\usage{

+foldIndexR(

+  sequence,

+  window = 51,

+  proteinName = NA,

+  pKaSet = "IPC_protein",

+  plotResults = TRUE

+)

+}

+\arguments{

+\item{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.}

+

+\item{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.}

+

+\item{proteinName}{character string with length = 1.

+optional setting to replace the name of the plot if plotResults = TRUE.}

+

+\item{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.}

+

+\item{plotResults}{logical value, TRUE by default.

+If \code{plotResults = TRUE} a plot will be the output.

+If \code{plotResults = FALSE} the output is a data frame with scores for

+each window analyzed.}

+

+\item{...}{any additional parameters, especially those for plotting.}

+}

+\value{

+see plotResults argument

+}

+\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. 

+  

+  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)\cr

+  \url{https://doi.org/10.1002/1097-0134(20001115)41:3<415::AID-PROT130>3.0.CO;2-7}

+  . \cr

+  

+  The FoldIndex method of using a sliding window and utilizing the uversky 

+  equation is described in Prilusky, J., Felder, C. E., et al. (2005). \cr

+  FoldIndex: a simple tool to predict whether a given protein sequence \cr 

+  is intrinsically unfolded. Bioinformatics, 21(16), 3435-3438. \cr

+}

+\section{Plot Colors}{

+

+  For users who wish to keep a common aesthetic, the following colors are

+  used when plotResults = TRUE. \cr

+  \itemize{

+  \item Dynamic line colors: \itemize{

+  \item Close to -1 = "#9672E6"

+  \item Close to 1 = "#D1A63F"

+  \item Close to midpoint = "grey65" or "#A6A6A6"}}

+   

+  @references

+  Kozlowski, L. P. (2016). IPC – Isoelectric Point Calculator. Biology

+  Direct, 11(1), 55. \url{https://doi.org/10.1186/s13062-016-0159-9} \cr

+  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. \cr

+  Prilusky, J., Felder, C. E., et al. (2005). \cr

+  FoldIndex: a simple tool to predict whether a given protein sequence \cr 

+  is intrinsically unfolded. Bioinformatics, 21(16), 3435-3438. \cr

+  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.

+  \url{https://doi.org/10.1002/1097-0134(20001115)41:3<415::AID-PROT130>3.0.CO;2-7}

+}

+

+\examples{

+#Amino acid sequences can be character strings

+aaString <- "ACDEFGHIKLMNPQRSTVWY"

+#Amino acid sequences can also be character vectors

+aaVector <- c("A", "C", "D", "E", "F",

+              "G", "H", "I", "K", "L",

+              "M", "N", "P", "Q", "R",

+              "S", "T", "V", "W", "Y")

+#Alternatively, .fasta files can also be used by providing

+  ##The path to the file as a character string.

+

+

+foldIndexR(aaVector)

+

+exampleDF <- 

+  foldIndexR(aaString,

+      plotResults = FALSE)

+head(exampleDF)

+

+}

+\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.

+}

+\seealso{

+\code{\link{KDNorm}} for residue hydropathy values.

+  See \code{\link{pKaData}} for residue pKa values and citations. See

+  \code{\link{hendersonHasselbalch}} for charge calculations.

+

+Other scaled hydropathy functions: 

+\code{\link{KDNorm}},

+\code{\link{meanScaledHydropathy}()},

+\code{\link{scaledHydropathyGlobal}()},

+\code{\link{scaledHydropathyLocal}()}

+}

+\concept{scaled hydropathy functions}

@@ -43,10 +43,11 @@ disorder based on environmental conditions. Regions of predicted

 environmental sensitivity are highlighted. See the respective functions

 for more details. This is skipped if uniprotAccession = NA.}

-\item{window}{a positive, odd integer. 7 by default.

+\item{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.}

+for each position along the sequence. 51 is default for 

+\code{\link{foldIndexR}}\cr.}

 \item{pH}{numeric value, 7.0 by default.

 The environmental pH used to calculate residue charge.}

@@ -94,6 +95,7 @@ The IDPRofile is a summation of many features of the idpr package,

   \code{\link{chargeCalculationLocal}}\cr

   \code{\link{scaledHydropathyLocal}}\cr

   \code{\link{structuralTendencyPlot}}\cr

+  \code{\link{foldIndexR}}\cr

   All of the above linked functions only require the sequence argument

   to output plots of characteristics associated with IDPs. The function also

   includes options for IUPred functions. The function does one of the

@@ -149,6 +151,19 @@ The IDPRofile is a summation of many features of the idpr package,

               Protein Science, 22(6), 693-724.

               doi:10.1002/pro.2261 }

     }

+    \item \code{\link{foldIndexR}}

+      \itemize{

+        \item{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.}

+         \item{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}

+        \item{Also see citations for hydrapthy and charge plots above}

+    }

     \item \code{\link{iupred}},

           \code{\link{iupredAnchor}},

           \code{\link{iupredRedox}}

@@ -194,6 +209,7 @@ idprofile(

   \code{\link{chargeCalculationLocal}}\cr

   \code{\link{scaledHydropathyLocal}}\cr

   \code{\link{structuralTendencyPlot}}\cr

+  \code{\link{foldIndexR}}\cr

   \code{\link{iupred}}\cr

   \code{\link{iupredAnchor}}\cr

   \code{\link{iupredRedox}}

@@ -46,6 +46,7 @@ Kyte, J., & Doolittle, R. F. (1982). A simple method for

 Other scaled hydropathy functions: 

 \code{\link{KDNorm}},

+\code{\link{foldIndexR}()},

 \code{\link{scaledHydropathyGlobal}()},

 \code{\link{scaledHydropathyLocal}()}

 }

@@ -87,6 +87,7 @@ Kyte, J., & Doolittle, R. F. (1982). A simple method for

 Other scaled hydropathy functions: 

 \code{\link{KDNorm}},

+\code{\link{foldIndexR}()},

 \code{\link{meanScaledHydropathy}()},

 \code{\link{scaledHydropathyLocal}()}

 }

@@ -105,6 +105,7 @@ Kyte, J., & Doolittle, R. F. (1982). A simple method for

 Other scaled hydropathy functions: 

 \code{\link{KDNorm}},

+\code{\link{foldIndexR}()},

 \code{\link{meanScaledHydropathy}()},

 \code{\link{scaledHydropathyGlobal}()}

 }

@@ -63,7 +63,15 @@ $$<R> = - 2.785 <H> + 1.151 $$

 This plot allows a distinction between

 negative and positive proteins while preserving the information of the 

-charge-hydropathy plot. 

+charge-hydropathy plot.

+

+Further, a this can be used to identify folded regions on a protein. 

+FoldIndex used this equation and set variables to 0 and using a sliding window, 

+the resulting values would identify regions predicted as folded or unfolded. 

+$$ Score = 2.785 <H> - \lvert<R>\rvert -1.151 $$

+When windows have a negative score (<0) sequences are predicted as disordered. 

+When windows have a positive score (>0) sequences are predicted as ordered. 

+This was described in Prilusky, J., Felder, C. E., et al. (2005). 

 ## Installation  

@@ -196,6 +204,15 @@ chargeHydropathyPlot(

 ```

+## Using FoldIndexR to predict folded and unfolded windows. 

+

+```{r}

+foldIndexR(sequence = HUMAN_P53,

+           plotResults = TRUE)

+```

+

+Prilusky, J., Felder, C. E., et al. (2005). 

+

 ## Calculating Scaled Hydropathy

 ### Mean Scaled Hydropathy

@@ -521,6 +538,11 @@ biology, 157(1), 105-132.

 Po, H. N., & Senozan, N. (2001). The Henderson-Hasselbalch equation:

 its history and limitations. Journal of Chemical Education, 78(11), 1499. 

+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. 

+

+

 Proteinogenic amino acid. (n.d.). In Wikipedia. Retrieved July 12th, 2020. 

 https://en.wikipedia.org/wiki/Proteinogenic_amino_acid#Chemical_properties

@@ -153,12 +153,13 @@ idprofile(sequence = P53_HUMAN,

 ```

-idprofile returns 4-5 plots:

+idprofile returns 5-6 plots:

  * Charge-Hydropathy Plot^\*^

  * Plot of Amino Acid Composition and Structural Tendency^†^

  * Calculations of Local Charge Along a Protein Sequence^\*^

  * Local, Scaled Hydropathy Along a Protein Sequence^\*^

+ * A prediction of intrinsic disorder by FoldIndex^\*^

  * A prediction of intrinsic disorder by IUPred2 (only with a uniprotAccession)^‡^

 *Detailed descriptions of each plot can be found in specific vignettes.*

@@ -173,7 +174,7 @@ idprofile returns 4-5 plots:

 A brief explanation of each plot is given below:

-### Charge-Hydropathy Plot

+### Charge-Hydropathy Plot and FoldIndex

 Uversky, Gillespie, & Fink (2000) showed that both high net charge and 

 low mean hydropathy are properties of IDPs (15). One explanation is that a high 

@@ -185,7 +186,11 @@ graphic can be used to distinguish proteins that are extended or compact under

 native conditions. However, it is important to note that IDPs can have the 

 characteristics of a collapsed protein or an extended protein. Therefore a 

 protein within the “collapsed protein” field does not necessary mean that it 

-lacks intrinsic disorder under native conditions (15, 31). 

+lacks intrinsic disorder under native conditions (15, 31). This equation was

+later applied to a method of predicting unfolded peptides using a sliding window 

+of charge and hydropathy in FoldIndex (44). When scores are negative, a region 

+is predicted as unfolded; when scores are positive, a region is predicted as 

+folded.

 **For further theory and details, please refer to idpr's **

@@ -387,6 +392,7 @@ et al. (2001) (25).

 41. Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL. NCBI BLAST: a better web interface. Nucleic Acids Research. 2008;36(suppl_2):W5-W9.

 42. Madeira F, Park YM, Lee J, Buso N, Gur T, Madhusoodanan N, et al. The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic acids research. 2019;47(W1):W636-W41.

 43. Pagès H, Aboyoun P, Gentleman R, DebRoy S. Biostrings: Efficient manipulation of biological strings. R package version. 2020;2(0).

+44. Prilusky J, Felder C, Zeev-Ben-Mordehai T, Rydberg E, Man O, Beckmann J, Silman I, & Sussman J. FoldIndex©: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics 21, no. 16 (2005): 3435-3438.