ligandmpnn

What problem does it solve?

This skill automates ligand-aware protein sequence design, enabling researchers to tailor amino-acid sequences around bound ligands for improved binding and function.

Core Features & Use Cases

• Ligand-context aware sequence design using LigandMPNN for small molecules, cofactors, and metal coordination sites.
• Suitable for designing around enzyme active sites and ligand-binding pockets to optimize activity and specificity.
• Flexible execution: Modal-based workflow (recommended) and local installation options for diverse research environments.

Quick Start

Use the LigandMPNN workflow to generate ligand-aware designs for a given protein-ligand complex. Example commands: modal run modal_ligandmpnn.py --pdb-path protein_ligand.pdb --num-seq-per-target 16 --sampling-temp 0.1 python run.py --pdb_path protein_ligand.pdb --out_folder output/ --num_seq_per_target 16