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

Rahaman, Jordon; Siltberg-Liberles, Jessica

Amino acid evolutionary rates (SEQ) for all sites across all alignments were aggregated and binned into four possible categories characterized by the distribution of PSIPRED predicted secondary structure at each site. Sites predicted to have a loop across all sequences are "conserved loops; C(L)" and sites predicted to have a helix across all sequences or a strand across all sequences are "conserved helix-strand; C(HS)" (table 3) . Sites predicted to have all three states (helix, strand, and loop) or any combination of loop and one other state are "non-conserved helix, loop, strand; NC(HLS)" and sites predicted to have a mixture of helix and strand are "nonconserved helix-strand; NC(HS)" (table 3) . In all cases, gaps were ignored when classifying combinations of secondary structure at a site or if secondary structure conservation exists at a particular site.