Extended Data Fig. 1. Combinatorial mutagenesis library 1 design and simulations.

a, Violin plot showing distributions of simulated AbundancePCA growth rates (assuming additivity of individual inferred folding free energy changes²³) versus number of random aa substitutions (n = 100,000) for PSD95-PDZ3. Violins are scaled to have the same maximum width. b, Simulated median AbundancePCA/BindingPCA growth rates of optimal combinatorial libraries of increasing maximum aa Hamming distances from the wild type. The horizontal dashed line indicates the 70th percentile of the maximal geometric mean (black). The vertical dashed line indicates the number of aa substitutions selected (n = 34) for the synthesized combinatorial mutagenesis library 1. c, Violin plot showing simulated distributions of AbundancePCA growth rates versus number of aa substitutions for combinatorial mutagenesis library 1. d, Similar to panel c but showing simulated distributions for BindingPCA growth rates. In panels c and d, the percentage of folded and bound protein variants (predicted fraction folded or bound molecules > 0.5) is shown at each Hamming distance from the wild type.