ligandmpnnlisted

# LigandMPNN Ligand-Aware Design ## Prerequisites | Requirement | Minimum | Recommended | |-------------|---------|-------------| | Python | 3.8+ | 3.10 | | CUDA | 11.0+ | 11.7+ | | GPU VRAM | 8GB | 16GB (T4) | | RAM | 8GB | 16GB | ## How to run > **First time?** See [Installation Guide](../../docs/installation.md) to set up Modal and biomodals. ### Option 1: Modal (recommended) ```bash cd biomodals modal run modal_ligandmpnn.py \ --pdb-path protein_ligand.pdb \ --num-seq-per-target 16 \ --sampling-temp 0.1 ``` **GPU**: T4 (16GB) | **Timeout**: 600s default ### Option 2: Local installation ```bash git clone https://github.com/dauparas/LigandMPNN.git cd LigandMPNN python run.py \ --pdb_path protein_ligand.pdb \ --out_folder output/ \ --num_seq_per_target 16 ``` ## Key parameters | Parameter | Default | Range | Description | |-----------|---------|-------|-------------| | `--pdb_path` | required | path | PDB with ligand | | `--num_seq_per_target` | 1 | 1-1000 | Sequences per structure | | `--sampling_temp` | "0.1" | "0.0001-1.0" | Temperature (string!) | | `--ligand_mpnn_use_side_chain_context` | true | bool | Use ligand context | ## Ligand Specification ### In PDB File Ligand must be present as HETATM records: ``` ATOM ...protein atoms... HETATM 1 C1 LIG A 999 x.xxx y.yyy z.zzz 1.00 0.00 C ``` ### Supported Ligand Types - Small molecules (HETATM) - Metals (Zn, Fe, Mg, Ca, etc.) - Cofactors (NAD, FAD, ATP) - DNA/RNA ## Output f