predictBinding: Predicts peptide:MHC-II binding interaction.

In Degoot123/PeptideMHC2Prediction: Prediction of Peptide:MHC-II Molecules Interactions

Description

This function predicts the outcome of interaction between peptide and mhc-ii molecule by calculating the energy of the binding from all possible configurations between the peptide and the mhc-ii ligand. It derives such configurations by using function getInputVector

Usage

predictBinding(pep, mhc_name, locus, opt = 1)

Arguments

pep	The amino acids sequence of the peptide of length =>9 nano mer.
mhc_name	The name of mhc-ii molecule.
locus	One of the three standard loci: DQ, DP, and DRB
opt	This parameter determines the prediction type (intra-allele or trans-alleles). 1 stands for intra-alleleic and 2 for trans-allelic. The default value of this is 1.

Value

A vector cantaining four items: the peptide, the mhc-ii molecule name, the probability of the binding, and the binary value (0 or 1), respectively.

Examples

predictBinding('AIGIITLYLGAVVQA', 'DRB1_1501',  'DRB', 1 )
predictBinding('ITKLGAKPDGKTDCT', 'DQB10201',  'DQ', 2)

Degoot123/PeptideMHC2Prediction documentation built on May 21, 2019, 10:15 a.m.