Including ligands restrains design of catalytically active residues

Summary

Including ligands during inverse folding allows amino acids in the binding pocket to be recovered at higher rates (1). For one test case, two of the three residues in a catalytic triad were not correctly predicted without ligand. However, inclusion of the ligand caused all three to be designed correctly.

Figures

Ref (1)

See also

• De novo structure prediction with ligands outperforms apo de novo structure prediction alone

1.

Dauparas J, Lee GR, Pecoraro R, An L, Anishchenko I, Glasscock C, et al. Atomic context-conditioned protein sequence design using LigandMPNN. Nature Methods. 2025;22(4):717–23. Available from: https://doi.org/10.1038/s41592-025-02626-1