LigandMPNN

LigandMPNN designs protein sequences and sidechain conformations in explicit atomic context of bound small molecules, nucleotides or metals, using fixed protein backbones and ligand coordinates from input PDBs. The API generates up to 2×1 sequences per request with optional sidechain repacking (up to 16 samples, 3 denoising steps), and reports overall and ligand-site confidence, per-residue log-probabilities and sequence recovery over redesigned residues. Typical uses include enzyme active-site design, small-molecule binders, sensors and DNA/RNA-binding interfaces.