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Significance Poor protein developability is a critical hindrance to biologic discovery and engineering. Experimental capacity limits variant analysis. We demonstrate the ability of an on-yeast protease assay, a split green fluorescent protein assay, and a split β-lactamase assay to predict recombinant protein production yields in bacteria. The assays presented increase the ability to measure protein developability by more than 100-fold over traditional approaches. Compared to models trained using sequence information alone, the assays are 35% more accurate and require 80% less data to achieve the same prediction accuracy. The assays were evaluated via randomized protein variants within a protein scaffold topology and offer a method to remove the limitation of variant developability quantification.

High-throughput developability assays enable library-scale identification of producible protein scaffold variants