Docking partners

Define 2 docking partners by uploading a PDB structure file.

Receptor

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Structure Sources

Structure file

Upload PDB structure file

If the PDB is a multi-model ensemble, specify the number of conformers

Generate harmonic modes

Number of modes to select

RMSD calculation

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

Definition of residues for HADDOCK-type distance restraints (optional)

Please supply residues as comma-separated lists of residue numbers

Active residues (directly involved in the interaction)

Passive residues (surrounding surface residues)

Ligand

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Structure Sources

Structure file

Upload PDB structure file

If the PDB is a multi-model ensemble, specify the number of conformers

Generate harmonic modes

Number of modes to select

RMSD calculation

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

Definition of residues for HADDOCK-type distance restraints (optional)

Please supply residues as comma-separated lists of residue numbers

Active residues (directly involved in the interaction)

Passive residues (surrounding surface residues)

Custom distance restraints

Custom distance restraints

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Harmonic distance restraints file (CNS/HADDOCK .tbl format)

Position restraints file (CNS/HADDOCK .tbl format)

Energy and Interaction

Energy and Interaction

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Perform grid-accelerated docking

Perform iATTRACT refinement after the docking

Which forcefield is to be used?

Forcefield

External tool for PDB completion and hydrogens
NOTE: PDB2PQR, AMBER and CNS require a local installation
NOTE: PDB2PQR only completes proteins; WHATIF is used for nucleic acids

PDB completion method

Analysis

Analysis

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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

Computation

Computation

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Please supply a name for your docking run (one word)

Name of the docking run

Number of processor cores