Fig 7. Sequence design with the opt-E protocol on the 60 antibody benchmark.

(A) Sequence recovery for amino acids in contact with the antigen and those not in contact with the antigen from the antigen-present and antigen-absent simulations. (B). Antigen risk ratios (ARRs) for the contacting and non-contacting residues. Values greater than 1.0 indicate that the native residue types were present in the design simulations in the presence of the antigen more often than they were present in the design simulations in the absence of the antigen.