Computational protocol: Identification and evaluation of the novel immunodominant antigen Rv2351c from Mycobacterium tuberculosis

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[…] T-cell epitopes were identified using TEpredict and other prediction tools from the IEDB-AR. The FASTA format of the amino-acid sequence of Rv2351c has been submitted to TEpredict and IEDB-AR (http://tools.iedb.org/mhci/). The human major histocompatibility complex (MHC) HLA-A and HLA-B alleles were used for the MHC class I antigen peptide binding. The binding affinity for the human MHC alleles that were obtained from prediction tools at IEDB-AR used the half-maximal inhibitory concentration of a biological substance (IC50) as the unit of measure. An IC50<50 nM indicates high affinity; IC50<500 nM indicates medium affinity; and IC50<5000 nM indicates low-affinity binding. A lower IC50 indicates a stronger binding affinity to the host MHC. The negative logarithm of IC50, pIC50, was used by TEpredict as the unit of measure to describe the strength of the binding affinity between the peptides and MHC molecules. A pIC50<6.3 (IC50>500 nM) indicates a low-binding affinity, a pIC50 in the range from 6.3 to 7.3 (50 nM7.3 (IC50<50 nM) indicates high-binding affinity. Nine-mer MHC class I T-cell epitope prediction was performed using the consensus method. Every epitope was predicted with an immunogenicity score using the T-cell pMHC class I immunogenicity predictor (http://tools.immuneepitope.org/immunogenicity/). […]

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