This PDF file includes:

• fig. S1. Structural comparisons of the ubiquitin backbone models.
• fig. S2. IC₅₀ and affinity validation of a subset of the designed ubiquitin variants against USP21.
• fig. S3. Venn diagrams of the designed ubiquitin variants recovered by phage display and Y2H.
• fig. S4. PCA of sequences identified by Y2H.
• fig. S5. Random forest regression model for sequence count prediction.
• fig. S6. Sequence logos of ubiquitin variants predicted to tightly bind USP21 by an ensemble of random forests model for variants derived from MD, CONCOORD, and Backrub.
• fig. S7. Y2H screening of ubiquitin library against USP21.
• table S1. Jenson-Shannon divergence of designed ubiquitin variants derived from MD, CONCOORD, and Backrub ensembles compared to the wild-type sequence and ubiquitin variants recovered from a biased naïve library.
• table S2. IC50 and associated deep sequencing read counts for four selected low-nanomolar binders to USP21.
• Legend for table S3
• table S4. Isothermal titration calorimetry of Ubv10 binding USP21.

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Other Supplementary Material for this manuscript includes the following:

• table S3 (Microsoft Excel format). Deep sequencing read counts of ubiquitin variants surviving phage display and Y2H selections.