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Define 2 docking partners by uploading a PDB structure file.
Structure file
If the PDB is a multi-model ensemble, specify the number of conformers
Number of modes to select
You can specify a PDB file to use as reference in RMSD calculations
Reference RMSD PDB file
What kind of molecule are you docking?
The PDB file contains all necessary atoms, including polar hydrogens
Please supply residues as comma-separated lists of residue numbers
Active residues (directly involved in the interaction)
Passive residues (surrounding surface residues)
Harmonic distance restraints file (CNS/HADDOCK .tbl format)
Position restraints file (CNS/HADDOCK .tbl format)
Perform grid-accelerated docking
Perform iATTRACT refinement after the docking
Which forcefield is to be used?
Forcefield
External tool for PDB completion and hydrogensNOTE: PDB2PQR, AMBER and CNS require a local installationNOTE: PDB2PQR only completes proteins; WHATIF is used for nucleic acids
PDB completion method
Calculate ligand RMSD after docking
Calculate interface RMSD after docking
Calculate fraction of native contacts after docking
Number of structures to collect as PDB file
Please supply a name for your docking run (one word)
Name of the docking run
Number of processor cores