This is the expert interface to the HADDOCK docking program. This interface provides more control over HADDOCK parameters and supports additional types of restraints.
Unfold the menus by clicking on the double arrows. Submit your job by providing your username and password and press submit.
For questions about the use of the HADDOCK portal please refer to: ask.bioexcel.eu
You may supply a name for your docking run (one word)
Name
First molecule
Structure definition
Where is the structure provided?
Which chain of the structure must be used?
PDB structure to submit
or: PDB code to download
Restraint definition
Data to drive the docking
Please supply residues as comma-separated lists of residue numbers
Active residues (directly involved in the interaction)
Passive residues (surrounding surface residues)
Define passive residues automatically around the active residues
Segment ID to use during the docking
What kind of molecule are you docking?
Histidine protonation states
Automatically guess histidine protonation states using molprobity
Histidines
First histidine
Residue number
Protonation state
Second histidine
Residue number
Protonation state
Third histidine
Residue number
Protonation state
Fourth histidine
Residue number
Protonation state
Fifth histidine
Residue number
Protonation state
Sixth histidine
Residue number
Protonation state
Seventh histidine
Residue number
Protonation state
Eighth histidine
Residue number
Protonation state
Ninth histidine
Residue number
Protonation state
Tenth histidine
Residue number
Protonation state
Semi-flexible segments
Side-chains and backbone of these residues will be allowed to move during semi-flexible refinement
How are the flexible segments defined
Semi-flexible segments
First segment
First number
Last number
Second segment
First number
Last number
Third segment
First number
Last number
Fourth segment
First number
Last number
Fifth segment
First number
Last number
Sixth segment
First number
Last number
Seventh segment
First number
Last number
Eighth segment
First number
Last number
Ninth segment
First number
Last number
Tenth segment
First number
Last number
Fully flexible segments
These segments will be allowed to move at all stages of it1
Fully flexible segments
First segment
First number
Last number
Second segment
First number
Last number
Third segment
First number
Last number
Fourth segment
First number
Last number
Fifth segment
First number
Last number
The N-terminus of your protein is positively charged
The C-terminus of your protein is negatively charged
Second molecule
Structure definition
Where is the structure provided?
Which chain of the structure must be used?
PDB structure to submit
or: PDB code to download
Restraint definition
Data to drive the docking
Please supply residues as comma-separated lists of residue numbers
Active residues (directly involved in the interaction)
Passive residues (surrounding surface residues)
Define passive residues automatically around the active residues
Segment ID to use during the docking
What kind of molecule are you docking?
Histidine protonation states
Automatically guess histidine protonation states using molprobity
Histidines
First histidine
Residue number
Protonation state
Second histidine
Residue number
Protonation state
Third histidine
Residue number
Protonation state
Fourth histidine
Residue number
Protonation state
Fifth histidine
Residue number
Protonation state
Sixth histidine
Residue number
Protonation state
Seventh histidine
Residue number
Protonation state
Eighth histidine
Residue number
Protonation state
Ninth histidine
Residue number
Protonation state
Tenth histidine
Residue number
Protonation state
Semi-flexible segments
Side-chains and backbone of these residues will be allowed to move during semi-flexible refinement
How are the flexible segments defined
Semi-flexible segments
First segment
First number
Last number
Second segment
First number
Last number
Third segment
First number
Last number
Fourth segment
First number
Last number
Fifth segment
First number
Last number
Sixth segment
First number
Last number
Seventh segment
First number
Last number
Eighth segment
First number
Last number
Ninth segment
First number
Last number
Tenth segment
First number
Last number
Fully flexible segments
These segments will be allowed to move at all stages of it1
Fully flexible segments
First segment
First number
Last number
Second segment
First number
Last number
Third segment
First number
Last number
Fourth segment
First number
Last number
Fifth segment
First number
Last number
The N-terminus of your protein is positively charged
The C-terminus of your protein is negatively charged
Distance restraints
If you specified that passive residues will be defined automatically, all surface residues will be selected within the following radius (in angstroms) around the active residues
Instead of specifying active and passive residues, you can supply a HADDOCK restraints TBL file (ambiguous restraints)
You can supply a HADDOCK restraints TBL file with restraints that will always be enforced (unambiguous restraints)
If one of your molecules is DNA/RNA, restraints are automatically created to preserve its structure.
Uncheck this option if you are docking with unstructured DNA/RNA
Create DNA/RNA restraints?
HADDOCK deletes by default all hydrogens except those bonded to a polar atom (N, O).
Uncheck this option if you have NOEs or other specific restraints to non-polar hydrogens
Remove non-polar hydrogens?
Random patches
Define randomly ambiguous interaction restraints from accessible residues
Center of mass restraints
Define center of mass restraints to enforce contact between the molecules
Force constant for center of mass contact restraints
Surface contact restraints
Define surface contact restraints to enforce contact between the molecules
Force constant for surface contact restraints
Random exclusion
Randomly exclude a fraction of the ambiguous restraints (AIRs)
Number of partitions for random exclusion (%excluded=100/number of partitions)
Sampling parameters
Number of structures for rigid body docking
Number of trials for rigid body minimisation
Sample 180 degrees rotated solutions during rigid body EM
Number of structures for semi-flexible refinement
Sample 180 degrees rotated solutions during semi-flexible SA
Solvent to use for the last iteration
Number of structures for the explicit solvent refinement
Epsilon constant for the electrostatic energy term
Note that for explicit solvent refinement cdie with epsilon=1 is used
Epsilon
Solvated docking mode
Perform solvated docking
Parameters for clustering
Clustering method (RMSD or Fraction of Common Contacts (FCC))
RMSD Cutoff for clustering (recommended: 7.5A for RMSD, 0.75 for FCC)
Minimum cluster size
Chain-Agnostic Algorithm (used for FCC clustering in symmetrical complexes)
fcc_ignc
Dihedral and hydrogen bond restraints
In addition to distance restraints, you may specify dihedral and hydrogen bond restraints
These restraints can be inter- or intramolecular
Dihedral angle restraints TBL file
Hydrogen bond restraints TBL file
Username and password
Username
Password