LigandMPNN (ligand-aware sequence design)

Overview

LigandMPNN (Dauparas et al. 2023; dauparas/LigandMPNN) extends ProteinMPNN's inverse folding to condition on non-protein context — small-molecule ligands, metal ions, and nucleic acids. Because the model sees the ligand/metal atoms, the residues it designs for a binding pocket or metal site are chosen to complement what is actually bound, which plain ProteinMPNN (protein-atoms-only) cannot do.

Use it whenever the design target is a site that contacts a ligand or ion. For sequence design of a backbone with no bound context, use alterlab-proteinmpnn.

When to Use This Skill