Baker, D.; Yang, W.; Hicks, D. R.; Ghosh, A.; Schwartze, T. A.; Coventry, B.; Goreshnik, I.; Allen, A.; Halabiya, S.; Kim, C.; Hinck, C. S.; Lee, D. S.; Bera, A.; Li, Z.; Wang, Y.; Schlichthaerle, T.; Cao, L.; Huang, B.; Garrett, S.; Gerben, S. R.; Rettie, S.; Heine, P.; Edman, N.; Murray, A. N.; Carter, L. P.; Stewart, L.; Almo, S.; Hinck, A. P.

While there has been progress in the de novo design of small globular miniproteins (50-65 residues) to bind to primarily concave regions of a target protein surface, computational design of minibinders to convex binding sites remains an outstanding challenge due to low level of overall shape complementarity. Here, we describe a general approach to generate computationally designed proteins which bind to convex target sites that employ geometrically matching concave scaffolds. We used this approach to design proteins binding to TGF{beta}RII, CTLA-4 and PD-L1 which following experimental optimization have low nanomolar to picomolar affinities and potent biological activity. Co-crystal structures of the TGF{beta}RII and CTLA-4 binders in complex with the receptors are in close agreement with the design models. Our approach provides a general route to generating very high affinity binders to convex protein target sites.