Our research tries to answer questions about the evolution of proteins and how this information can be used to create a new range of AI tools. The tools we have developed make it possible to predict the structure of protein interactions, and to design new molecules that bind to proteins.

We aim to create a universal molecular framework, where any molecule can be predicted. We are deploying the technology we develop and test it in the lab to create new molecular functions.

Binder design

Li Q, Vlachos E.N., Bryant P. Design of linear and cyclic peptide binders of different lengths only from a protein target sequence. bioRxiv. 2024. p. 2024.06.20.599739. doi:10.1101/2024.06.20.599739 Paper Code

Bryant P., Elofsson A. Peptide binder design with inverse folding and protein structure prediction. Communications Chemistry. 2023; 6: 229. Paper

Bryant P., Elofsson A. EvoBind: in silico directed evolution of peptide binders with AlphaFold. bioRxiv. 2022. p. 2022.07.23.501214. doi:10.1101/2022.07.23.501214 Paper

Linear         Cyclic


Structure prediction of protein-ligand complexes

Bryant, P., Kelkar, A., Guljas, A. Clementi, C. and Noé F. Structure prediction of protein-ligand complexes from sequence information with Umol. Nat Commun 15, 4536 (2024). https://doi.org/10.1038/s41467-024-48837-6 Paper Code


Structure prediction of alternative protein conformations

Bryant P, Noé F. Structure prediction of alternative protein conformations. Nat Commun 15, 7328 (2024). Paper Code


Structure prediction of protein complexes

Bryant P, Noé F. Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile. PLoS Comput Biol. (2024);20: e1012253. Paper Code

Bryant, P., Pozzati, G., Zhu, W. et al. Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search. Nat Commun 13, 6028 (2022). Paper Code

Bryant P., Pozzati G., Elofsson A. Improved prediction of protein-protein interactions using AlphaFold2. Nat Commun 13: 1–11 (2022). Paper Code Better code

Burke, D.F.^, Bryant, P.^, Barrio-Hernandez, I.^ et al. Towards a structurally resolved human protein interaction network. Nat Struct Mol Biol (2023). https://doi.org/10.1038/s41594-022-00910-8 Paper