2.3. Pipeline Recap

This marks the end of the bulk pipeline, which is responsible for screening and suggesting a few promising candidates. As we’ve just seen, the pipeline gathers a lot of initial data (step 1), then removes proteins with a low probability of being a good antigen through several filters. The filters can be built by first thinking about the attributes of a good antigen. In step 2, all proteins not shared across most strains were removed, as a good antigen would be vital and conserved against A. baumannii subspecies. In step 3, we removed proteins that were too similar to human or gut microbiome ones in order to minimize the risk of a vaccine causing major harm to human subjects. In step 4, we used the fact that an antigen is easily reachable and filtered out proteins that are found inside bacterial cells only. Lastly, in step 5, we ensure suggested candidates are similar enough to proteins linked to virulence that are also essential for the functioning of bacteria, which lowers the chance of developing resistance against antibodies targeting the antigens. Overall, filters are somewhat lax to account for the potential error a bioinformatics tool produces - still, by getting proteins through multiple ones, a manageable list of suggestions can be created. With some manual curation, some of the suggested candidates can then be tested in a lab.