Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses

Rahaman, Jordon; Siltberg-Liberles, Jessica

For all protein families, secondary structure elements were predicted using PSIPRED (McGuffin et al. 2000) and JPred (Drozdetskiy et al. 2015) . For most protein families, the disagreement between secondary structure predictors is greater than for the disorder predictors (table 1). In fact, 15 of the 17 protein families compared disagree at more than 10% of alignment sites, and two of these disagree at more than 20% of sites. To compare the binary structureto-loop transitions (SLT), QCR was estimated as a measure of association for SLT based on the different predictors. In general, there is a moderate positive association between SLT for PSIPRED vs. SLT for JPred that is weaker than for the different DOT comparisons (table 2) . It should be noted that SLT does not differentiate between alpha helix and beta strand, but considers both as "structure." This is a correct assumption if protein structure is conserved and consistently predicted, but for some protein families that is not the case.