Docking partners

Define protein and peptide by uploading a PDB structure file and a sequence.

Protein

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Structure Sources

Structure file

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

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)

RMSD calculation

You can specify a PDB file to use as reference in RMSD calculations

Reference RMSD PDB file

Peptide

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Structure Sources

Peptide sequence

Give peptide sequence in single letter code

RMSD calculation

You can specify a PDB file to use as reference in RMSD calculations

Reference RMSD PDB file

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