Guide · Screening
Molecular docking
Prepare a receptor and one or more ligands, define the binding site search box, run AutoDock Vina, and review ranked poses.
Prerequisites
A cleaned protein in your project (see the Protein cleaning guide) At least one ligand — SMILES string, SDF file, or drawn in Ketcher
Step 1: Add a ligand to the molecule library
Go to Molecules → Import. Paste a SMILES string (e.g. CC1=CC=CC=C1) or upload an SDF file. For a new structure, click Edit in Ketcher to draw the molecule from scratch. Ligand-X generates a 3D conformer automatically using RDKit.
Step 2: Run pocket finding (or define a custom box)
From your cleaned protein, click Find pockets. The pocket finder (fpocket) ranks candidate binding sites by druggability score and marks each with a transparent surface in the viewer. Select the pocket you want to target, or click Manual box to drag a custom search volume directly in the viewer.
Step 3: Open the docking job form
With a pocket selected, click Dock. The form pre-fills the receptor path, search box coordinates, and box size from the pocket. Verify they look correct in the preview panel.
Step 4: Select ligands and configure Vina
Choose one or more ligands from your molecule library for this run. Under Vina parameters, set exhaustiveness (default 8), max poses (default 9), and energy range. Higher exhaustiveness is slower but finds more diverse poses.
Step 5: Submit the docking job
Click Run docking. Each ligand is prepared with Meeko (adds charges, sets rotatable bonds) and docked independently. Job progress streams to the jobs panel.
Step 6: Review poses and interactions
When complete, click Results. Poses are ranked by Vina affinity score (kcal/mol). Click any pose to load it in the Mol* viewer. The interactions panel lists predicted hydrogen bonds, hydrophobics, and pi contacts. Use the pose switcher to compare conformations.
Step 7: Export and continue
Download a pose as .sdf for external analysis, or click Send to MD to use this docked complex as the starting structure for a molecular dynamics simulation.
Expected outputs
Ranked pose list with Vina affinity scores SDF files for each pose Interaction summary (H-bonds, hydrophobics, pi contacts)
Tips
If scores are all worse than −5 kcal/mol, the search box may be misplaced — try increasing box size or running pocket finding again. For fragment screening, set exhaustiveness to 4 to increase throughput; for lead optimisation, use 16+.