alterlab-ligandmpnn

# 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 Use this skill when the user wants to: - Design a **small-molecule binding pocket** so the residues fit the ligand. - Design a **metal-coordinating site** (e.g. Zn/Fe) with the ion in context. - Redesign residues that **contact a ligand, ion, or nucleic acid**. - Do **enzyme active-site** design where the substrate/cofactor should guide the choice. ### Does NOT Trigger | Scenario | Use instead | |----------|-------------| | Sequence design for a backbone with **no** ligand/metal context | `alterlab-proteinmpnn` | | **Generate** a backbone or scaffold a functional motif | `alterlab-rfdiffusion` | | Validate a design by refolding | `alterlab-alphafold` | | Co-fold the protein WITH the ligand from scratch | `alterlab-boltz` | | Dock a ligand into a fixed pocket (pose, not sequence) | `alterlab-diffdock` | ## Core Capabil...