Structure-based discovery
Molecular docking workspace
Run P2Rank-guided AutoDock Vina workflows from a PDB structure and ligand SMILES, then inspect the ranked complex in a browser-based 3D viewer.
VinaReproducible pose generation
P2RankBinding pocket detection
3DInteractive complex inspection
Queued computation
Configure a docking run
The calculation continues on the scientific worker while this page reports progress.
The interactive protein and ligand complex will appear here.
Native PyMOL output
Ray-traced best-pose image
This image is rendered by headless PyMOL on the docking worker. The orange structure is the docked ligand; the green structure is the crystallographic reference when available.
| Rank | Box | Affinity | RMSD | Cluster | Pose file |
|---|
Docking scores and poses are computational research outputs. Experimental validation is required before biological interpretation.
Calculation path
From structure to inspectable complex
Each run is isolated, resource-limited and retained as a downloadable archive for reproducibility.
- Prepare
Retrieve the PDB structure, select chains, clean the receptor and generate ligand coordinates. - Detect and dock
Use the native ligand, P2Rank pockets or global boxes to run AutoDock Vina. - Rank and inspect
Return affinities, clusters and pose files with an interactive protein-ligand view.