Binding strength prediction
In netmhc2pan: Interface to 'NetMHCIIpan'

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

This demo shows how to predict the binding strength of peptides to different Major Histocompatibility Class II (MHC-II) haplotypes.

First load the library:

library(netmhc2pan)

This demo assumes NetMHCIIpan is installed. Installation cannot be done netmhc2pan, as one needs to request a download link for version 3.2 at https://services.healthtech.dtu.dk/services/NetMHCIIpan-3.2/.

To install netmhc2pan, use install_netmhc2pan with the download link:

install_netmhc2pan("https://www.cbs.dtu.dk/download/33A6B0AC-0F2E-11E9-B4D1-8ABCB9CD16B5/")
install_netmhc2pan("https://richelbilderbeek.nl/tmp_netMHCIIpan-3.2.Linux.tar.gz")

The installation of netmhc2pan is checked, with the goal of producing a helpful error message:

tryCatch(
  check_netmhc2pan_installation(),
  error = function(e) print(e)
)

Now, lets use the sequence of an example protein:

sequence <- "FAMILYVWFAMILYV"
message(sequence)

Now, we need to select an MHC-II haplotype. There are many alleles, so first we count the number of haplotypes:

if (is_netmhc2pan_installed()) {
  mhc_haplotypes <- get_netmhc2pan_alleles()
  length(mhc_haplotypes)
}

Now, we simply pick the first haplotype:

if (is_netmhc2pan_installed()) {
  mhc_haplotype <- mhc_haplotypes[1]
}

Now, we can predict how strong our peptide binds to our allele, by obtaining the Inhibitory Concentration 50% (IC50) value in nanomolars (nM), of which lower values indicate stronger binders:

if (is_netmhc2pan_installed()) {
  knitr::kable(
    predict_ic50(
      peptides = sequence,
      mhc_haplotype = mhc_haplotype
    )
  )

}

To investigate if whole a protein is immunogenic, we need to obtain the IC50 values for all its cleaved products. As the MHC-II molecules prefers 13 amino acids residues, we can get the IC50 values for each residue as such:

if (is_netmhc2pan_installed()) {
  knitr::kable(
    predict_ic50s(
      protein_sequence = "AVLWAGVAFLAFLQLTALVLNLL",
      peptide_length = 13,
      mhc_haplotype = mhc_haplotype
    )
  )

}