solublempnnlisted

# SolubleMPNN Solubility-Optimized 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) SolubleMPNN uses the ProteinMPNN Modal wrapper with soluble model: ```bash cd biomodals modal run modal_proteinmpnn.py \ --pdb-path backbone.pdb \ --num-seq-per-target 16 \ --sampling-temp 0.1 \ --model-name v_48_020 ``` **GPU**: T4 (16GB) | **Timeout**: 600s default ### Option 2: Local installation ```bash git clone https://github.com/dauparas/ProteinMPNN.git cd ProteinMPNN # Use soluble model weights python protein_mpnn_run.py \ --pdb_path backbone.pdb \ --out_folder output/ \ --num_seq_per_target 16 \ --sampling_temp "0.1" \ --model_name "v_48_020" # Soluble model ``` ## Key parameters | Parameter | Default | Range | Description | |-----------|---------|-------|-------------| | `--pdb_path` | required | path | Input structure | | `--num_seq_per_target` | 1 | 1-1000 | Sequences per structure | | `--sampling_temp` | "0.1" | "0.0001-1.0" | Temperature (string!) | | `--model_name` | v_48_020 | string | Soluble model variant | ## Model Variants | Model | Description | Use Case | |-------|-------------|----------| | v_48_002 | Standard | General design | | v_48_020