Check Signal peptide fidelity

A convenience function to compute atomic contacts between a predicted signal peptide and the rest of the protein in AlphaFold2 structures. This implements the FORTRAN code from Elcock-Lab/AlphaFold2-Signal, with added features to calculate the median pLDDT and count residues surpassing the pLDDT threshold for the signal peptide. Unlike the FORTRAN version, this function highlights cases where low-confidence signal peptide structures filter all residues, suggesting they may not represent true outward-facing signal peptides.

Usage

easyAF2Signal(pdb, cut_dist = 4, nsignal = 25, bfac_thresh = 90, nskip = 1)

Arguments

pdb

A link to PDB file or path to PDB file if the file is locally present.

cut_dist

Distance cutoff for defining atomic contacts (Default: 4 Angstroms).

nsignal

Number of residues that comprise of N-terminal signal peptide. If SignalP prediction is available for your protein, the predicted length should be used. (Default: 25).

bfac_thresh

pLDDT threshold for including residues in the atomic contact calculation.

nskip

No. of residues immediately next to the cleavage site to exclude from atomic contact calculations.

Value

A data frame, containing statistics about signal peptide and rest of the protein. Zero atomic or residue-residue contact is indicative of True positives while non-zero values are putative False Positives.

Examples

if (FALSE) { # \dontrun{
df <- easyAF2Signal("https://alphafold.ebi.ac.uk/files/AF-Q9TY95-F1-model_v4.pdb")
} # }