2.11. Prediction of the BL Epitope

To identify potential continuous epitopes capable of stimulating a BL response, we used the artificial neural network-based ABCpred tool [70]. The cutoff threshold was set to 0.90, which allowed for a greater specificity to be selected. To predict potential discontinuous BL epitopes, Discotope v2.0 [71] (server version) (http://www.cbs.dtu.dk/services/DiscoTope/, accessed on 20 July 2020) was used. The cutoff threshold and specificity were set to −2.5 and 80%, respectively.

This prediction included both SP and NP, which were extracted from the RCSB PDB with the following identifiers: 6lzg, 6m0j, 6vw1, 6w41, 6yla, 6yor, 6csb, 6vxx, 6vyb, 6m3m, 6vyo and 6wkp. Predictions resulting from the algorithms were considered to be potential epitopes. The peptide with the highest ABCpred score was also chosen with a partial or total presence in the experimental sequences identified as SARS-CoV immunological targets in IEBD with a 90% BLAST alignment. Also, it was located in potentially immunogenic regions, either because they were shown in Discotope-provided areas from various experimental structures or because they were contained in a specific protein domain. The antigenic peptides with values >0.4 in Vaxijen that were non-toxic and non-allergenic according to AlgPred [72] (http://crdd.osdd.net/raghava/algpred/submission.html, accessed on 25 July 2020) were chosen as potential BL epitopes and were added to the multi-epitope construct.