Molecular Docking
Upload a receptor PDB and ligand SDF/mol2 file to run AutoDock Vina and visualise the docked complex in 3D.
System Limitations
Uses rigid receptor (AutoDock Vina). Results for flexible binding sites may underestimate affinity by 2–3 kcal/mol.
Nuclear hormone receptors
ER, AR, MR, GR, PR
Require flexible receptor — Vina rigid underestimates by 2–3 kcal/mol
Metalloprotease active sites
MMP, ADAM, ACE
Zn²⁺/Fe coordination ignored by Vina scoring function
GPCRs
β2-AR, D2, CXCR4
Transmembrane binding pocket poorly sampled by rigid docking
Very large ligands
MW > 600 Da
Too many rotatable bonds → exhaustiveness 16 insufficient
Apo structures
No HETATM in PDB
Falls back to fpocket — box center may not match binding site
Recent Docking Jobs
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Validated Test Pairs
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Expected ΔG: −5 to −7 weak · −7 to −9 moderate · −9 to −12 strong · below −12 suspicious