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Input data
Input parameters
Docking parameters
search
Job name
Number of molecules
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
arrow_drop_down
Molecule 1 - input
Which chain of the structure must be used?
All
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Only atoms with the specified chain ID will be considered
PDB structure to submit
Files in PDB or mmCIF format only
What kind of molecule are you docking?
Protein or Protein-Ligand
Ligand
Peptide
Glycan
Nucleic acid (DNA and/or RNA)
Protein-Nucleic acid
Shape
Dummy
Do you want to coarse-grain your molecule?
Convert all-atom structures into Martini coarse-grained ones.
Is it a cyclic peptide?
Fix molecule at its original position during it0?
Segment ID to use during the docking
This segment ID will be associated to the whole molecule
The N-terminus of your protein is positively charged
The C-terminus of your protein is negatively charged
Keep terminal phosphates for nucleic acids
arrow_drop_down
Molecule 2 - input
Which chain of the structure must be used?
All
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Only atoms with the specified chain ID will be considered
PDB structure to submit
Files in PDB or mmCIF format only
What kind of molecule are you docking?
Protein or Protein-Ligand
Ligand
Peptide
Glycan
Nucleic acid (DNA and/or RNA)
Protein-Nucleic acid
Shape
Dummy
Do you want to coarse-grain your molecule?
Convert all-atom structures into Martini coarse-grained ones.
Is it a cyclic peptide?
Fix molecule at its original position during it0?
Segment ID to use during the docking
This segment ID will be associated to the whole molecule
The N-terminus of your protein is positively charged
The C-terminus of your protein is negatively charged
Keep terminal phosphates for nucleic acids
arrow_drop_down
Molecule 3 - input
Which chain of the structure must be used?
All
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Only atoms with the specified chain ID will be considered
PDB structure to submit
Files in PDB or mmCIF format only
What kind of molecule are you docking?
Protein or Protein-Ligand
Ligand
Peptide
Glycan
Nucleic acid (DNA and/or RNA)
Protein-Nucleic acid
Shape
Dummy
Do you want to coarse-grain your molecule?
Convert all-atom structures into Martini coarse-grained ones.
Is it a cyclic peptide?
Fix molecule at its original position during it0?
Segment ID to use during the docking
This segment ID will be associated to the whole molecule
The N-terminus of your protein is positively charged
The C-terminus of your protein is negatively charged
Keep terminal phosphates for nucleic acids
arrow_drop_down
Molecule 4 - input
Which chain of the structure must be used?
All
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Only atoms with the specified chain ID will be considered
PDB structure to submit
Files in PDB or mmCIF format only
What kind of molecule are you docking?
Protein or Protein-Ligand
Ligand
Peptide
Glycan
Nucleic acid (DNA and/or RNA)
Protein-Nucleic acid
Shape
Dummy
Do you want to coarse-grain your molecule?
Convert all-atom structures into Martini coarse-grained ones.
Is it a cyclic peptide?
Fix molecule at its original position during it0?
Segment ID to use during the docking
This segment ID will be associated to the whole molecule
The N-terminus of your protein is positively charged
The C-terminus of your protein is negatively charged
Keep terminal phosphates for nucleic acids
arrow_drop_down
Molecule 5 - input
Which chain of the structure must be used?
All
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Only atoms with the specified chain ID will be considered
PDB structure to submit
Files in PDB or mmCIF format only
What kind of molecule are you docking?
Protein or Protein-Ligand
Ligand
Peptide
Glycan
Nucleic acid (DNA and/or RNA)
Protein-Nucleic acid
Shape
Dummy
Do you want to coarse-grain your molecule?
Convert all-atom structures into Martini coarse-grained ones.
Is it a cyclic peptide?
Fix molecule at its original position during it0?
Segment ID to use during the docking
This segment ID will be associated to the whole molecule
The N-terminus of your protein is positively charged
The C-terminus of your protein is negatively charged
Keep terminal phosphates for nucleic acids
arrow_drop_down
Molecule 6 - input
Which chain of the structure must be used?
All
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Only atoms with the specified chain ID will be considered
PDB structure to submit
Files in PDB or mmCIF format only
What kind of molecule are you docking?
Protein or Protein-Ligand
Ligand
Peptide
Glycan
Nucleic acid (DNA and/or RNA)
Protein-Nucleic acid
Shape
Dummy
Do you want to coarse-grain your molecule?
Convert all-atom structures into Martini coarse-grained ones.
Is it a cyclic peptide?
Fix molecule at its original position during it0?
Segment ID to use during the docking
This segment ID will be associated to the whole molecule
The N-terminus of your protein is positively charged
The C-terminus of your protein is negatively charged
Keep terminal phosphates for nucleic acids
arrow_drop_down
Molecule 7 - input
Which chain of the structure must be used?
All
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Only atoms with the specified chain ID will be considered
PDB structure to submit
Files in PDB or mmCIF format only
What kind of molecule are you docking?
Protein or Protein-Ligand
Ligand
Peptide
Glycan
Nucleic acid (DNA and/or RNA)
Protein-Nucleic acid
Shape
Dummy
Do you want to coarse-grain your molecule?
Convert all-atom structures into Martini coarse-grained ones.
Is it a cyclic peptide?
Fix molecule at its original position during it0?
Segment ID to use during the docking
This segment ID will be associated to the whole molecule
The N-terminus of your protein is positively charged
The C-terminus of your protein is negatively charged
Keep terminal phosphates for nucleic acids
arrow_drop_down
Molecule 8 - input
Which chain of the structure must be used?
All
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Only atoms with the specified chain ID will be considered
PDB structure to submit
Files in PDB or mmCIF format only
What kind of molecule are you docking?
Protein or Protein-Ligand
Ligand
Peptide
Glycan
Nucleic acid (DNA and/or RNA)
Protein-Nucleic acid
Shape
Dummy
Do you want to coarse-grain your molecule?
Convert all-atom structures into Martini coarse-grained ones.
Is it a cyclic peptide?
Fix molecule at its original position during it0?
Segment ID to use during the docking
This segment ID will be associated to the whole molecule
The N-terminus of your protein is positively charged
The C-terminus of your protein is negatively charged
Keep terminal phosphates for nucleic acids
arrow_drop_down
Molecule 9 - input
Which chain of the structure must be used?
All
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Only atoms with the specified chain ID will be considered
PDB structure to submit
Files in PDB or mmCIF format only
What kind of molecule are you docking?
Protein or Protein-Ligand
Ligand
Peptide
Glycan
Nucleic acid (DNA and/or RNA)
Protein-Nucleic acid
Shape
Dummy
Do you want to coarse-grain your molecule?
Convert all-atom structures into Martini coarse-grained ones.
Is it a cyclic peptide?
Fix molecule at its original position during it0?
Segment ID to use during the docking
This segment ID will be associated to the whole molecule
The N-terminus of your protein is positively charged
The C-terminus of your protein is negatively charged
Keep terminal phosphates for nucleic acids
arrow_drop_down
Molecule 10 - input
Which chain of the structure must be used?
All
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Only atoms with the specified chain ID will be considered
PDB structure to submit
Files in PDB or mmCIF format only
What kind of molecule are you docking?
Protein or Protein-Ligand
Ligand
Peptide
Glycan
Nucleic acid (DNA and/or RNA)
Protein-Nucleic acid
Shape
Dummy
Do you want to coarse-grain your molecule?
Convert all-atom structures into Martini coarse-grained ones.
Is it a cyclic peptide?
Fix molecule at its original position during it0?
Segment ID to use during the docking
This segment ID will be associated to the whole molecule
The N-terminus of your protein is positively charged
The C-terminus of your protein is negatively charged
Keep terminal phosphates for nucleic acids
arrow_drop_down
Molecule 11 - input
Which chain of the structure must be used?
All
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Only atoms with the specified chain ID will be considered
PDB structure to submit
Files in PDB or mmCIF format only
What kind of molecule are you docking?
Protein or Protein-Ligand
Ligand
Peptide
Glycan
Nucleic acid (DNA and/or RNA)
Protein-Nucleic acid
Shape
Dummy
Do you want to coarse-grain your molecule?
Convert all-atom structures into Martini coarse-grained ones.
Is it a cyclic peptide?
Fix molecule at its original position during it0?
Segment ID to use during the docking
This segment ID will be associated to the whole molecule
The N-terminus of your protein is positively charged
The C-terminus of your protein is negatively charged
Keep terminal phosphates for nucleic acids
arrow_drop_down
Molecule 12 - input
Which chain of the structure must be used?
All
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Only atoms with the specified chain ID will be considered
PDB structure to submit
Files in PDB or mmCIF format only
What kind of molecule are you docking?
Protein or Protein-Ligand
Ligand
Peptide
Glycan
Nucleic acid (DNA and/or RNA)
Protein-Nucleic acid
Shape
Dummy
Do you want to coarse-grain your molecule?
Convert all-atom structures into Martini coarse-grained ones.
Is it a cyclic peptide?
Fix molecule at its original position during it0?
Segment ID to use during the docking
This segment ID will be associated to the whole molecule
The N-terminus of your protein is positively charged
The C-terminus of your protein is negatively charged
Keep terminal phosphates for nucleic acids
arrow_drop_down
Molecule 13 - input
Which chain of the structure must be used?
All
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Only atoms with the specified chain ID will be considered
PDB structure to submit
Files in PDB or mmCIF format only
What kind of molecule are you docking?
Protein or Protein-Ligand
Ligand
Peptide
Glycan
Nucleic acid (DNA and/or RNA)
Protein-Nucleic acid
Shape
Dummy
Do you want to coarse-grain your molecule?
Convert all-atom structures into Martini coarse-grained ones.
Is it a cyclic peptide?
Fix molecule at its original position during it0?
Segment ID to use during the docking
This segment ID will be associated to the whole molecule
The N-terminus of your protein is positively charged
The C-terminus of your protein is negatively charged
Keep terminal phosphates for nucleic acids
arrow_drop_down
Molecule 14 - input
Which chain of the structure must be used?
All
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Only atoms with the specified chain ID will be considered
PDB structure to submit
Files in PDB or mmCIF format only
What kind of molecule are you docking?
Protein or Protein-Ligand
Ligand
Peptide
Glycan
Nucleic acid (DNA and/or RNA)
Protein-Nucleic acid
Shape
Dummy
Do you want to coarse-grain your molecule?
Convert all-atom structures into Martini coarse-grained ones.
Is it a cyclic peptide?
Fix molecule at its original position during it0?
Segment ID to use during the docking
This segment ID will be associated to the whole molecule
The N-terminus of your protein is positively charged
The C-terminus of your protein is negatively charged
Keep terminal phosphates for nucleic acids
arrow_drop_down
Molecule 15 - input
Which chain of the structure must be used?
All
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Only atoms with the specified chain ID will be considered
PDB structure to submit
Files in PDB or mmCIF format only
What kind of molecule are you docking?
Protein or Protein-Ligand
Ligand
Peptide
Glycan
Nucleic acid (DNA and/or RNA)
Protein-Nucleic acid
Shape
Dummy
Do you want to coarse-grain your molecule?
Convert all-atom structures into Martini coarse-grained ones.
Is it a cyclic peptide?
Fix molecule at its original position during it0?
Segment ID to use during the docking
This segment ID will be associated to the whole molecule
The N-terminus of your protein is positively charged
The C-terminus of your protein is negatively charged
Keep terminal phosphates for nucleic acids
arrow_drop_down
Molecule 16 - input
Which chain of the structure must be used?
All
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Only atoms with the specified chain ID will be considered
PDB structure to submit
Files in PDB or mmCIF format only
What kind of molecule are you docking?
Protein or Protein-Ligand
Ligand
Peptide
Glycan
Nucleic acid (DNA and/or RNA)
Protein-Nucleic acid
Shape
Dummy
Do you want to coarse-grain your molecule?
Convert all-atom structures into Martini coarse-grained ones.
Is it a cyclic peptide?
Fix molecule at its original position during it0?
Segment ID to use during the docking
This segment ID will be associated to the whole molecule
The N-terminus of your protein is positively charged
The C-terminus of your protein is negatively charged
Keep terminal phosphates for nucleic acids
arrow_drop_down
Molecule 17 - input
Which chain of the structure must be used?
All
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Only atoms with the specified chain ID will be considered
PDB structure to submit
Files in PDB or mmCIF format only
What kind of molecule are you docking?
Protein or Protein-Ligand
Ligand
Peptide
Glycan
Nucleic acid (DNA and/or RNA)
Protein-Nucleic acid
Shape
Dummy
Do you want to coarse-grain your molecule?
Convert all-atom structures into Martini coarse-grained ones.
Is it a cyclic peptide?
Fix molecule at its original position during it0?
Segment ID to use during the docking
This segment ID will be associated to the whole molecule
The N-terminus of your protein is positively charged
The C-terminus of your protein is negatively charged
Keep terminal phosphates for nucleic acids
arrow_drop_down
Molecule 18 - input
Which chain of the structure must be used?
All
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Only atoms with the specified chain ID will be considered
PDB structure to submit
Files in PDB or mmCIF format only
What kind of molecule are you docking?
Protein or Protein-Ligand
Ligand
Peptide
Glycan
Nucleic acid (DNA and/or RNA)
Protein-Nucleic acid
Shape
Dummy
Do you want to coarse-grain your molecule?
Convert all-atom structures into Martini coarse-grained ones.
Is it a cyclic peptide?
Fix molecule at its original position during it0?
Segment ID to use during the docking
This segment ID will be associated to the whole molecule
The N-terminus of your protein is positively charged
The C-terminus of your protein is negatively charged
Keep terminal phosphates for nucleic acids
arrow_drop_down
Molecule 19 - input
Which chain of the structure must be used?
All
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Only atoms with the specified chain ID will be considered
PDB structure to submit
Files in PDB or mmCIF format only
What kind of molecule are you docking?
Protein or Protein-Ligand
Ligand
Peptide
Glycan
Nucleic acid (DNA and/or RNA)
Protein-Nucleic acid
Shape
Dummy
Do you want to coarse-grain your molecule?
Convert all-atom structures into Martini coarse-grained ones.
Is it a cyclic peptide?
Fix molecule at its original position during it0?
Segment ID to use during the docking
This segment ID will be associated to the whole molecule
The N-terminus of your protein is positively charged
The C-terminus of your protein is negatively charged
Keep terminal phosphates for nucleic acids
arrow_drop_down
Molecule 20 - input
Which chain of the structure must be used?
All
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Only atoms with the specified chain ID will be considered
PDB structure to submit
Files in PDB or mmCIF format only
What kind of molecule are you docking?
Protein or Protein-Ligand
Ligand
Peptide
Glycan
Nucleic acid (DNA and/or RNA)
Protein-Nucleic acid
Shape
Dummy
Do you want to coarse-grain your molecule?
Convert all-atom structures into Martini coarse-grained ones.
Is it a cyclic peptide?
Fix molecule at its original position during it0?
Segment ID to use during the docking
This segment ID will be associated to the whole molecule
The N-terminus of your protein is positively charged
The C-terminus of your protein is negatively charged
Keep terminal phosphates for nucleic acids
Note: You should expect a short waiting time when submitting your parameters depending on the size of the PDB files you are providing.
Proudly powered by:
This work is co-funded by the Horizon 2020 projects
EOSC-hub
and
EGI-ACE
(grant numbers
777536
and
101017567
),
BioExcel
(grant numbers
823830
,
675728
and
101093290
)
and by a computing grant from
NWO-ENW
(project number 2019.053).
