Multi-state design of flexible proteins predicts sequences optimal for conformational change
Fig 6
Root mean square deviations of residue mutation frequencies of influenza A subtypes and HA2 profiles predicted by RECON MSD and SSD.
(A) Dendrogram of root mean square deviations (RMSD) of influenza A subtype HA2 profiles sorted by pairwise RMSD. The mutation frequencies derived from the multiple sequence alignment profile of each influenza A subtype was compared to all other subtypes by calculating the mean standard deviation of each aligned position’s mean sum of squared differences of all twenty amino acid frequencies with respect to each other subtype profile. Pairwise RMSD values were sorted to form clades, with the height along the y axis indicating the pairwise RMSD between each clade. (B) RMSD of each IVR subtype multiple sequence alignment (MSA) profile with respect to RECON MSD and SSD. The x axis represents each IVR subtype profile sorted as in Panel A. The y axis represents the RMSD, calculated in the same fashion as in Panel A, of each subtype profile in relation to either RECON MSD or SSD.