Computational Design of Novel Protein-Protein Interactions with Therapeutic Potential

A. Marchand, S. Buckley, A. Schneuing, M. Pacesa, M. Elia, P. Gainza, E. Elizarova, R. M. Neeser, P. W. Lee, L. Reymond, Y. Miao, L. Scheller, S. Georgeon, J. Schmidt, P. Schwaller, S. J. Maerkl, M. Bronstein, B. Correia “Targeting protein–ligand neosurfaces with a generalizable deep learning tool“ Nature 2025. [DOI]

G. M. P. Giordano Attianese, S. Shui, E. Cribioli, M. Triboulet, L. Scheller, M. Hafezi, P. Reichenbach, P. Gainza, S. Georgeon, B. Correia, M. Irving “Dual ON/OFF-switch chimeric antigen receptor controlled by two clinically approved drugs“ Proc. Natl. Acad. Sci. U.S.A. 2024. [DOI]

D. Chen, X. Zhang, A. A. Vorobieva, R. Tachibana, A. Stein, R. P. Jakob, Z. Zou, D. A. Graf, A. Li, T. Maier, B. Correia, T. R. Ward “An evolved artificial radical cyclase enables the construction of bicyclic terpenoid scaffolds via an H-atom transfer pathway“ Nat. Chem. 2024. [DOI]

D. Listov, C. A. Goverde, B. Correia, S. J. Fleishman “Opportunities and challenges in design and optimization of protein function“ Nat. Rev. Mol. Cell Biol. 2024. [DOI]

C. A. Goverde, M. Pacesa, N. Goldbach, L. J. Dornfeld, P. E. M. Balbi, S. Georgeon, S. Rosset, S. Kapoor, J. Choudhury, J. Dauparas, C. Schellhaas, S. Kozlov, D. Baker, S. Ovchinnikov, A. J. Vecchio, B. Correia “Computational design of soluble and functional membrane protein analogues“ Nature 2024. [DOI]

H. Khakzad, I. Igashov, A. Schneuing, C. Goverde, M. Bronstein, B. Correia “A new age in protein design empowered by deep learning“ Cell Syst. 2023. [DOI]

S. Shui, L. Scheller, B. Correia “Protein-based bandpass filters for controlling cellular signaling with chemical inputs“ Nat. Chem. Biol. 2023. [DOI]

I. Masuho, R. Kise, P. Gainza, E. Von Moo, X. Li, R. Tany, H. Wakasugi-Masuho, B. Correia, K. A. Martemyanov “Rules and mechanisms governing G protein coupling selectivity of GPCRs“ Cell Rep. 2023. [DOI]

S. Shui, S. Buckley, L. Scheller, B. Correia “Rational design of small-molecule responsive protein switches“ Protein Sci. 2023. [DOI]

P. Gainza, S. Wehrle, A. Van Hall-Beauvais, A. Marchand, A. Scheck, Z. Harteveld, S. Buckley, D. Ni, S. Tan, F. Sverrisson, C. Goverde, P. Turelli, C. Raclot, A. Teslenko, M. Pacesa, S. Rosset, S. Georgeon, J. Marsden, A. Petruzzella, K. Liu, Z. Xu, Y. Chai, P. Han, G. F. Gao, E. Oricchio, B. Fierz, D. Trono, H. Stahlberg, M. Bronstein, B. Correia “De novo design of protein interactions with learned surface fingerprints“ Nature 2023. [DOI]

K. M. Castro, A. Scheck, S. Xiao, B. E. Correia “Computational design of vaccine immunogens“ Curr. Opin. Biotechnol. 2022. [DOI]

J. Wang, S. Lisanza, D. Juergens, D. Tischer, J. L. Watson, K. M. Castro, R. Ragotte, A. Saragovi, L. F. Milles, M. Baek, I. Anishchenko, W. Yang, D. R. Hicks, M. Expòsit, T. Schlichthaerle, J. Chun, J. Dauparas, N. Bennett, B. I. M. Wicky, A. Muenks, F. DiMaio, B. Correia, S. Ovchinnikov, D. Baker “Scaffolding protein functional sites using deep learning“ Science 2022. [DOI]

A. Marchand, A. K. Van Hall-Beauvais, B. Correia “Computational design of novel protein–protein interactions – An overview on methodological approaches and applications“ Curr. Opin. Struct. Biol. 2022. [DOI]

A. Scheck, S. Rosset, M. Defferrard, A. Loukas, J. Bonet, P. Vandergheynst, B. Correia “RosettaSurf—A surface-centric computational design approach“ PLoS Comput. Biol. 2022. [DOI]

S. Shui, P. Gainza, L. Scheller, C. Yang, Y. Kurumida, S. Rosset, S. Georgeon, R. B. Di Roberto, R. Castellanos-Rueda, S. Reddy, B. Correia “A rational blueprint for the design of chemically-controlled protein switches“ Nat. Commun. 2021. [DOI]