This is the guru interface to the HADDOCK docking program. This interface provides full control over HADDOCK parameters and supports a wide range of experimental 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)
Do you want to define a radius of gyration restraint (e.g from SAXS)?
Radius of gyration
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
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
Noncrystallographic symmetry restraints
NCS parameters
Use this type of restraints
Force constant
Segment pair
Segment pair 1
Segment
Segment 1
First number
Last number
Segment ID
Segment 2
First number
Last number
Segment ID
Segment pair 2
Segment
Segment 1
First number
Last number
Segment ID
Segment 2
First number
Last number
Segment ID
Segment pair 3
Segment
Segment 1
First number
Last number
Segment ID
Segment 2
First number
Last number
Segment ID
Segment pair 4
Segment
Segment 1
First number
Last number
Segment ID
Segment 2
First number
Last number
Segment ID
Segment pair 5
Segment
Segment 1
First number
Last number
Segment ID
Segment 2
First number
Last number
Segment ID
Symmetry restraints
Symmetry parameters
Use this type of restraints
Force constant
C2 symmetry segment pair
C2 symmetry segment pair 1
Segment
Segment 1
First number
Last number
Segment ID
Segment 2
First number
Last number
Segment ID
C2 symmetry segment pair 2
Segment
Segment 1
First number
Last number
Segment ID
Segment 2
First number
Last number
Segment ID
C2 symmetry segment pair 3
Segment
Segment 1
First number
Last number
Segment ID
Segment 2
First number
Last number
Segment ID
C2 symmetry segment pair 4
Segment
Segment 1
First number
Last number
Segment ID
Segment 2
First number
Last number
Segment ID
C2 symmetry segment pair 5
Segment
Segment 1
First number
Last number
Segment ID
Segment 2
First number
Last number
Segment ID
C2 symmetry segment pair 6
Segment
Segment 1
First number
Last number
Segment ID
Segment 2
First number
Last number
Segment ID
C2 symmetry segment pair 7
Segment
Segment 1
First number
Last number
Segment ID
Segment 2
First number
Last number
Segment ID
C2 symmetry segment pair 8
Segment
Segment 1
First number
Last number
Segment ID
Segment 2
First number
Last number
Segment ID
C2 symmetry segment pair 9
Segment
Segment 1
First number
Last number
Segment ID
Segment 2
First number
Last number
Segment ID
C2 symmetry segment pair 10
Segment
Segment 1
First number
Last number
Segment ID
Segment 2
First number
Last number
Segment ID
C3 symmetry segment triple
C3 symmetry segment triple 1
Segment
Segment 1
First number
Last number
Segment ID
Segment 2
First number
Last number
Segment ID
Segment 3
First number
Last number
Segment ID
C3 symmetry segment triple 2
Segment
Segment 1
First number
Last number
Segment ID
Segment 2
First number
Last number
Segment ID
Segment 3
First number
Last number
Segment ID
C4 symmetry segment quadruple
C4 symmetry segment quadruple 1
Segment
Segment 0
First number
Last number
Segment ID
Segment 1
First number
Last number
Segment ID
Segment 2
First number
Last number
Segment ID
Segment 3
First number
Last number
Segment ID
C4 symmetry segment quadruple 2
Segment
Segment 0
First number
Last number
Segment ID
Segment 1
First number
Last number
Segment ID
Segment 2
First number
Last number
Segment ID
Segment 3
First number
Last number
Segment ID
C5 symmetry segment quintuple
C5 symmetry segment quintuple 1
Segment
Segment 1
First number
Last number
Segment ID
Segment 2
First number
Last number
Segment ID
Segment 3
First number
Last number
Segment ID
Segment 4
First number
Last number
Segment ID
Segment 5
First number
Last number
Segment ID
Restraints energy constants
Energy constants for unambiguous restraints
Iterations:
0: Rigid body EM (it0)
1: Semi-flexible SA (it1)
2: Water refinement
First iteration (0-2)
Last iteration (0-2)
Energy constants per stage
hot
cool1
cool2
cool3
Energy constants for ambiguous restraints
Iterations:
0: Rigid body EM (it0)
1: Semi-flexible SA (it1)
2: Water refinement
First iteration (0-2)
Last iteration (0-2)
Energy constants per stage
hot
cool1
cool2
cool3
Energy constants for hydrogen bond restraints
Iterations:
0: Rigid body EM (it0)
1: Semi-flexible SA (it1)
2: Water refinement
First iteration (0-2)
Last iteration (0-2)
Energy constants per stage
hot
cool1
cool2
cool3
Energy constants for dihedral angle restraints
hot
cool1
cool2
cool3
Automatically define backbone dihedral restraints from structure?
Energy constants for radius-of-gyration restraints
hot
cool1
cool2
cool3
Atom selections for the radius of gyration restraint
Residual dipolar couplings
Residual dipolar couplings 1
RDC type
R
D
SANI energy constants
Iterations:
0: Rigid body EM (it0)
1: Semi-flexible SA (it1)
2: Water refinement
First iteration (0-2)
Last iteration (0-2)
Energy constants per stage
hot
cool1
cool2
cool3
VEAN energy constants
ini_bor energy constants per stage
hot
cool1
cool2
cool3
fin_bor energy constants per stage
hot
cool1
cool2
cool3
ini_cen energy constants per stage
hot
cool1
cool2
cool3
fin_cen energy constants per stage
hot
cool1
cool2
cool3
HADDOCK TBL file containing RDC restraints
RDC file
Residual dipolar couplings 2
RDC type
R
D
SANI energy constants
Iterations:
0: Rigid body EM (it0)
1: Semi-flexible SA (it1)
2: Water refinement
First iteration (0-2)
Last iteration (0-2)
Energy constants per stage
hot
cool1
cool2
cool3
VEAN energy constants
ini_bor energy constants per stage
hot
cool1
cool2
cool3
fin_bor energy constants per stage
hot
cool1
cool2
cool3
ini_cen energy constants per stage
hot
cool1
cool2
cool3
fin_cen energy constants per stage
hot
cool1
cool2
cool3
HADDOCK TBL file containing RDC restraints
RDC file
Residual dipolar couplings 3
RDC type
R
D
SANI energy constants
Iterations:
0: Rigid body EM (it0)
1: Semi-flexible SA (it1)
2: Water refinement
First iteration (0-2)
Last iteration (0-2)
Energy constants per stage
hot
cool1
cool2
cool3
VEAN energy constants
ini_bor energy constants per stage
hot
cool1
cool2
cool3
fin_bor energy constants per stage
hot
cool1
cool2
cool3
ini_cen energy constants per stage
hot
cool1
cool2
cool3
fin_cen energy constants per stage
hot
cool1
cool2
cool3
HADDOCK TBL file containing RDC restraints
RDC file
Residual dipolar couplings 4
RDC type
R
D
SANI energy constants
Iterations:
0: Rigid body EM (it0)
1: Semi-flexible SA (it1)
2: Water refinement
First iteration (0-2)
Last iteration (0-2)
Energy constants per stage
hot
cool1
cool2
cool3
VEAN energy constants
ini_bor energy constants per stage
hot
cool1
cool2
cool3
fin_bor energy constants per stage
hot
cool1
cool2
cool3
ini_cen energy constants per stage
hot
cool1
cool2
cool3
fin_cen energy constants per stage
hot
cool1
cool2
cool3
HADDOCK TBL file containing RDC restraints
RDC file
Residual dipolar couplings 5
RDC type
R
D
SANI energy constants
Iterations:
0: Rigid body EM (it0)
1: Semi-flexible SA (it1)
2: Water refinement
First iteration (0-2)
Last iteration (0-2)
Energy constants per stage
hot
cool1
cool2
cool3
VEAN energy constants
ini_bor energy constants per stage
hot
cool1
cool2
cool3
fin_bor energy constants per stage
hot
cool1
cool2
cool3
ini_cen energy constants per stage
hot
cool1
cool2
cool3
fin_cen energy constants per stage
hot
cool1
cool2
cool3
HADDOCK TBL file containing RDC restraints
RDC file
Pseudo Contact Shifts restraints
Tensor distance restraints file for all PCS restraints
PCS restraints 1
PCS type
PCS energy constants
Iterations:
0: Rigid body EM (it0)
1: Semi-flexible SA (it1)
2: Water refinement
First iteration (0-2)
Last iteration (0-2)
Energy constants per stage
hot
cool1
cool2
cool3
R
D
PCS file
PCS restraints 2
PCS type
PCS energy constants
Iterations:
0: Rigid body EM (it0)
1: Semi-flexible SA (it1)
2: Water refinement
First iteration (0-2)
Last iteration (0-2)
Energy constants per stage
hot
cool1
cool2
cool3
R
D
PCS file
PCS restraints 3
PCS type
PCS energy constants
Iterations:
0: Rigid body EM (it0)
1: Semi-flexible SA (it1)
2: Water refinement
First iteration (0-2)
Last iteration (0-2)
Energy constants per stage
hot
cool1
cool2
cool3
R
D
PCS file
PCS restraints 4
PCS type
PCS energy constants
Iterations:
0: Rigid body EM (it0)
1: Semi-flexible SA (it1)
2: Water refinement
First iteration (0-2)
Last iteration (0-2)
Energy constants per stage
hot
cool1
cool2
cool3
R
D
PCS file
PCS restraints 5
PCS type
PCS energy constants
Iterations:
0: Rigid body EM (it0)
1: Semi-flexible SA (it1)
2: Water refinement
First iteration (0-2)
Last iteration (0-2)
Energy constants per stage
hot
cool1
cool2
cool3
R
D
PCS file
PCS restraints 6
PCS type
PCS energy constants
Iterations:
0: Rigid body EM (it0)
1: Semi-flexible SA (it1)
2: Water refinement
First iteration (0-2)
Last iteration (0-2)
Energy constants per stage
hot
cool1
cool2
cool3
R
D
PCS file
PCS restraints 7
PCS type
PCS energy constants
Iterations:
0: Rigid body EM (it0)
1: Semi-flexible SA (it1)
2: Water refinement
First iteration (0-2)
Last iteration (0-2)
Energy constants per stage
hot
cool1
cool2
cool3
R
D
PCS file
PCS restraints 8
PCS type
PCS energy constants
Iterations:
0: Rigid body EM (it0)
1: Semi-flexible SA (it1)
2: Water refinement
First iteration (0-2)
Last iteration (0-2)
Energy constants per stage
hot
cool1
cool2
cool3
R
D
PCS file
PCS restraints 9
PCS type
PCS energy constants
Iterations:
0: Rigid body EM (it0)
1: Semi-flexible SA (it1)
2: Water refinement
First iteration (0-2)
Last iteration (0-2)
Energy constants per stage
hot
cool1
cool2
cool3
R
D
PCS file
PCS restraints 10
PCS type
PCS energy constants
Iterations:
0: Rigid body EM (it0)
1: Semi-flexible SA (it1)
2: Water refinement
First iteration (0-2)
Last iteration (0-2)
Energy constants per stage
hot
cool1
cool2
cool3
R
D
PCS file
Relaxation anisotropy restraints
Anisotropy restraints 1
Anisotropy type
DANI energy constants
Iterations:
0: Rigid body EM (it0)
1: Semi-flexible SA (it1)
2: Water refinement
First iteration (0-2)
Last iteration (0-2)
Energy constants per stage
hot
cool1
cool2
cool3
Correlation time
D
R
H frequency
N frequency
Anisotropy file
Anisotropy restraints 2
Anisotropy type
DANI energy constants
Iterations:
0: Rigid body EM (it0)
1: Semi-flexible SA (it1)
2: Water refinement
First iteration (0-2)
Last iteration (0-2)
Energy constants per stage
hot
cool1
cool2
cool3
Correlation time
D
R
H frequency
N frequency
Anisotropy file
Anisotropy restraints 3
Anisotropy type
DANI energy constants
Iterations:
0: Rigid body EM (it0)
1: Semi-flexible SA (it1)
2: Water refinement
First iteration (0-2)
Last iteration (0-2)
Energy constants per stage
hot
cool1
cool2
cool3
Correlation time
D
R
H frequency
N frequency
Anisotropy file
Anisotropy restraints 4
Anisotropy type
DANI energy constants
Iterations:
0: Rigid body EM (it0)
1: Semi-flexible SA (it1)
2: Water refinement
First iteration (0-2)
Last iteration (0-2)
Energy constants per stage
hot
cool1
cool2
cool3
Correlation time
D
R
H frequency
N frequency
Anisotropy file
Anisotropy restraints 5
Anisotropy type
DANI energy constants
Iterations:
0: Rigid body EM (it0)
1: Semi-flexible SA (it1)
2: Water refinement
First iteration (0-2)
Last iteration (0-2)
Energy constants per stage
hot
cool1
cool2
cool3
Correlation time
D
R
H frequency
N frequency
Anisotropy file
Energy and interaction parameters
Nonbonded parameters
Do you want to include dihedral angle energy terms?
These are independent of dihedral angle restraints
Include dihedral angle restraints
Do you want to include the electrostatic energy term for docking?
Note that it will be automatically included in the solvent refinement
Include electrostatic during rigid body docking (it0)
Include electrostatic during semi-flexible SA (it1)
Use constant (cdie) or distance-dependent (rdie) dielectric
Scaling of intermolecular interactions for rigid body EM
Scaling of intermolecular interactions for semi-flexible SA (it1)
Initial value
Rigid body dynamic
SA with flexible side-chains (cool2)
SA with flexible backbone and side-chains (cool3)
Final value
Rigid body dynamic
SA with flexible side-chains (cool2)
SA with flexible backbone and side-chains (cool3)
Scoring parameters
Define the weights for the various terms for the sorting of structures (scoring)
1: Rigid body EM (it0)
2: semi-flexible SA (it1)
3: water refinement
Evdw
Evdw 1
Evdw 2
Evdw 3
Eelec
Eelec 1
Eelec 2
Eelec 3
Eair
Eair 1
Eair 2
Eair 3
Erg
Erg 1
Erg 2
Erg 3
Esani
Esani 1
Esani 2
Esani 3
Exrdc
Exrdc 1
Exrdc 2
Exrdc 3
Expcs
Expcs 1
Expcs 2
Expcs 3
Edani
Edani 1
Edani 2
Edani 3
Evean
Evean 1
Evean 2
Evean 3
Ecdih
Ecdih 1
Ecdih 2
Ecdih 3
Esym
Esym 1
Esym 2
Esym 3
BSA
BSA 1
BSA 2
BSA 3
dEint
dEint 1
dEint 2
dEint 3
Edesolv
Edesolv 1
Edesolv 2
Edesolv 3
Advanced sampling parameters
Do you want to cross-dock all combinations in the ensembles of starting structures?
Turn off this option if you only want to dock structure 1 of ensemble A
to structure 1 of ensemble B, structure 2 to structure 2, etc.
Perform cross-docking
Enable this option to multiply the number of structures in all iterations by the number of starting structure combinations.
The number of combinations depends on the cross-docking parameter.
If cross-docking is disabled, the number of combinations is the size of the first ensemble.
If cross-docking is enabled, the number of combinations is the sizes of all ensembles multiplied.
Multiply the number of calculated structures by all combinations
Randomize starting orientations
Perform initial rigid body minimisation
Allow translation in rigid body minimisation
initial seed for random number generator
it1 parameters
temperature for rigid body high temperature TAD
initial temperature for rigid body first TAD cooling step
final temperature after first cooling step
initial temperature for second TAD cooling step with flexible side-chain at the inferface
final temperature after second cooling step
initial temperature for third TAD cooling step with fully flexible interface
final temperature after third cooling step
time step
factor for timestep in TAD
number of MD steps for rigid body high temperature TAD
number of MD steps during first rigid body cooling stage
number of MD steps during second cooling stage with flexible side-chains at interface
number of MD steps during third cooling stage with fully flexible interface
final solvated refinement
number of steps for heating phase (100, 200, 300K)
number of steps for 300K phase
number of steps for cooling phase (300, 200, 100K)
calculate explicit desolvation energy (note this will double the cpu requirements)
Solvated docking parameters
Solvated docking can be enabled in the Sampling Parameters section
Which method to use for solvating?
db: database-based (recommended), restraints: for restrained solvating to amino-acid most often forming
Method
Which propensity database to use?
Statistical: based on an analysis of water-mediated contacts in the PDB, Kyte-Doolittle: based on the Kyte-Doolittle hydrophobicity scale
Database method
Initial cutoff for restraints solvating method
Cutoff for restraints solvating method
Scale factor for restraints solvating method
This is the fraction of all interface water after the initial rigid body docking that will be kept (note that more waters might be removed if the interaction energy is unfavorable)
Fraction of water to keep in ntrial loop
This is the fraction of interface water involving DNA phosphates after the initial rigid body docking that will be kept (note that more waters might be removed if the interaction energy is unfavorable)
Fraction of water to keep in ntrial loop for DNA phosphates
Additional random fraction of water to keep in ntrial loop
Water-surface-cutoff
Do some water analysis
Use translation in loop miniwater
How many different solvation shells to generate
Analysis parameters
Number of structures to analyze
Cutoff distance (proton-acceptor) to define an hydrogen bond
Cutoff distance (carbon-carbon) to define an hydrophobic contact
After the final solvent refinement, write additional PDB files including solvent
Username and password
Username
Password