# Docking: DiffDock-L A diffusion-based molecular docking lab built on **DiffDock-L v1.1.3**. Provide a receptor PDB and a ligand SMILES (or RDKit-readable file), get back diffusion-sampled poses ranked by confidence. ## What it simulates - DiffDock-L inference in managed runtime mode: clones the pinned upstream repo, builds a venv, caches both for later runs. - Multiple diffusion samples scored with a confidence model. - Bundled `1a0q` receptor and SMILES ligand so a fresh run docks without setup. - Pose table, confidence summary, and the merged top-ranked complex.  ## Run it on the Hub 1. Open the [DiffDock: DiffDockLDockingPredictor Lab](https://hub.biosimulant.com/labs/5bb4fd94-ca5c-4fac-b314-2bc5b5d527c2) on the public Hub. 2. Click **Run**. The bundled `1a0q` defaults dock without any parameter editing. ## Inputs you can tune | Input | Meaning | |---|---| | `protein_path` | Receptor PDB file. Defaults to `data/1a0q/1a0q_protein_processed.pdb`. | | `ligand_description` | SMILES string or path to an RDKit-readable ligand file. | | `run_options.samples_per_complex` | Number of DiffDock samples to draw. | | `run_options.inference_steps` | Denoising steps per sample. | | `run_options.batch_size` | Inference batch size. | | `run_options.save_visualisation` | Whether to write per-step reverse-process PDBs. | ## What results to expect - **Pose ranking table**: rank, DiffDock confidence (unitless log-likelihood-style score), confidence band (`high`, `moderate`, or `low`), and the SDF filename. - **3D structure view**: receptor with the top pose merged in as `top_rank_complex.pdb`. - **Confidence summary**: top-pose score, band, total pose count, and every per-pose confidence so bimodal pose distributions are visible. - **Run metadata**: runtime mode, cache directories, executed command, returncode, truncated stdout/stderr, and `status: completed` / `status: error`. The lab exposes generated PDB and SDF files through `structure_artifacts`, so remote runs upload them as durable run artifacts before completion.  **Info:** Source on GitHub: [models-diffdock](https://github.com/Biosimulant/models-diffdock). See [Artifact Outputs](/references/library/artifact-outputs) for the file-output contract. The first run needs internet access (clones the upstream repo and downloads model checkpoints); later runs are offline.