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. Author manuscript; available in PMC: 2022 May 24.
Published in final edited form as: J Chem Inf Model. 2021 Apr 26;61(5):2368–2382. doi: 10.1021/acs.jcim.1c00056

Figure 9.

Figure 9.

Logoplots showing the relative frequency of mutations for experimentally validated immunogenic peptides in deimmunized and non-deimmunized designs of P99 β-lactamase (PDB ID 1XX2). Letters above the horizontal line are seen more frequently in deimmunized designs (n=500), whereas letters below the horizontal line are seen more frequently in the standard Rosetta designs (n=500). Grey lettering above the logoplot indicates the native sequence, with the orange, underlined residues indicating positions that have been mutated in experimentally validated deimmunization campaigns.18 Designs with no PSSM-based restrictions are shown in panels A-C, and designs with base 2 log-odds PSSM-based restrictions of 1 for the same epitopes are shown in panels D-F. See also Figure S19–Figure S21 for corresponding plots for other protein targets.