Docking partners

Define 2 docking partners by uploading a PDB structure file.

Receptor

Restore default values

Structure Sources

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

Ligand

Restore default values

Structure Sources

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

Custom distance restraints

Custom distance restraints

Restore default values

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

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