Docking partners

Define up to 10 docking partners by uploading a PDB structure file or identifying them by their RCSB Protein Databank ID. Ensemble structures are allowed.

Docking partner 1

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Structure Sources

Structure file

Name of the grid for this molecule

Which chain must be used?

What kind of molecule are you docking?

Use harmonic modes

Or: generate harmonic modes automatically

Use all-atom contact spring constants in mode generation

Number of modes to select

Use ensembles

Number of conformers in the ensemble

Ensemble search

RMSD calculation

You can specify a PDB file to use as reference in RMSD calculations
Leave blank to use the docked PDB instead (bound conformation = unbound conformation)

Reference RMSD PDB file

It is possible to specify alternative references

Alternative RMSD PDB file

Alternative RMSD PDB file 2

Definition of residues for HADDOCK AIR restraints (optional)

Please supply residues as comma-separated lists of residue numbers

Active residues (directly involved in the interaction)

Passive residues (surrounding surface residues)

The PDB file contains all necessary atoms, including polar hydrogens

Add charged termini to each chain

Grids

Grid 1

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Name of this grid

Plateau distance (A) for grid calculation

Neighbor list cutoff (A) for grid calculation

Do you want to calculate the grid on multiple cores using OpenMP?

Calculate grid using OpenMP?

Is the grid a torque grid?

torque

Calculate long-range potentials on the grid

Iteration

Iteration 1

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The nonbonded pairlist distance cutoff (rcut) (in A**2) during this iteration

rcut

The maximum number of energy minimization or Monte Carlo steps (vmax)

vmax

Trajectory mode: only minimize the first structure, and output the structure after every minimization step

Trajectory mode

Preparation mode: only minimizes the orientation of the molecules, without forcefield

Preparation mode

Distance restraint weight

Enable Monte Carlo mode

Temperature (in kT)

Rotation step size (in radians)

Translation step size (in angstroms)

Mode deformation step size (in angstroms)

Probability to switch between ensemble conformers

Sampling

Sampling

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Fix the receptor during docking

Docking search

Number of structures for random search

Initial distance from center (radius) for random search

Custom search files
For a custom search, supply a starting structures file, OR: rotations and/or translations files

Custom search files

Starting structures file for custom search

Rotations file for custom search

Translations file for custom search

Distance restraints files

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

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

Position restraints file (CNS/HADDOCK .tbl format)

Weight of all distance restraints during scoring

If you used flexibility in the form of normal modes or iATTRACT, you may choose remove the deformations (de-mode) after the docking

De-mode

iATTRACT parameters

Perform iATTRACT refinement after the docking

Number of structures to refine

Distance cutoff for flexible residues

Energy and Interaction

Energy and Interaction

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Gravity

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

PDB completion method

Restraining force constant for gravity and non-generative symmetry

Restraining force constant for harmonic distance restraints

Restraining force constant for AIRs and custom HADDOCK restraints

Fraction of AIRs and HADDOCK restraints removed at random

Soft-square parameter (maximum violation after which the force becomes linear) for custom HADDOCK restraints

Restraining force constant for position restraints

Which forcefield is to be used?

Forcefield

In ghost mode, the forcefield is turned off

Enable ghost mode, forcefield is turned off

In ghost-ligands mode, the forcefield is turned off between ligands (all partners beyond the first)

Enable ghost-ligands mode

Epsilon constant for the electrostatic energy term

Epsilon

Use constant (cdie) or distance-dependent (rdie) dielectric

Atom density grids

Atom density grid 1

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Voxel size (A)

Grid dimension (voxels)

Force constant

Symmetry

You can use generative symmetry or distance-restrained symmetry. If you want to use generative symmetry:

  • Provide an explicit symmetry axis and origin
  • Specify a single reference symmetry partner
  • In the Docking Partner section, only define the reference partner structure
If you want to use distance-restrained symmetry:
  • Do not provide explicit symmetry axis and origin
  • Specify all symmetry partners that are to be restrained
  • In the Docking Partner section, specify all partner structures, which must be identical

Symmetry 1

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Generative symmetry axis

Origin for generative symmetry axis

X

X

Y

Y

Z

Z

Symmetry type

Symmetry fold (2-fold, 3-fold, ...)

Symmetry partners

1

2

3

4

5

6

7

8

9

10

11

12

Analysis

Analysis

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Perform a rescoring step after docking

Sort the final structures according to forcefield energy

Remove redundant structures after docking

Ignore ensemble conformers for redundancy

If you perform RMSD analysis, you may remove all flexibility (ensemble and modes) beforehand

Remove flexibility

Calculate ligand RMSD after docking

Which atoms to use in RMSD calculation

Calculate interface RMSD after docking

Calculate fraction of native contacts after docking

Collect the structures as PDBs after docking

The nonbonded pairlist distance cutoff (rcut) (in A**2) during rescoring

rcut (rescoring)

Number of structures to collect

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

Number of structures in a single job (leave blank to divide all structures equally over the cores)

Header for docking protocol script

Footer for docking protocol script