HADDOCK - Input form

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HADDOCK submission

Distance restraints

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

Use tight center of mass restraints?

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)

Radius of gyration restraint

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

Perform final refinement?

Refine with short molecular dynamics in explicit solvent?

Solvent to use

Number of structures for the final refinement

Number of structures to analyze

Solvated docking mode

Perform solvated docking

Cutoff for defining neighbouring flexible regions

Definition of flexible segments of neighboring residues of contacts

Clustering parameters

Clustering method (RMSD or Fraction of Common Contacts (FCC))

RMSD Cutoff for clustering (recommended: 7.5A for RMSD, 0.60 for FCC)

Minimum cluster size

Chain-Agnostic Algorithm (used for FCC clustering in symmetrical complexes)

Dihedral and hydrogen bonds restraints

In addition to distance restraints, you may specify dihedral and hydrogen bond restraints. These restraints can be inter- or intra-molecular.

Dihedral angle restraints TBL file

Hydrogen bond restraints TBL file

Automatically define backbone dihedral restraints from structure?

Error bound for the dihedral restraints (in degrees)

Noncrystallographic symmetry restraints

Use NCS restraints

Force constant

Number of segment pairs

NCS Segment pair 1

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

NCS Segment pair 2

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

NCS Segment pair 3

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

NCS Segment pair 4

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

NCS Segment pair 5

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

NCS Segment pair 6

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

NCS Segment pair 7

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

NCS Segment pair 8

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

NCS Segment pair 9

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

NCS Segment pair 10

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

NCS Segment pair 11

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Symmetry restraints

Use symmetry restraints

Force constant

Number of C2 symmetry segment pairs

Number of C3 symmetry segment pairs

Number of C4 symmetry segment pairs

Number of C5 symmetry segment pairs

Number of C6 symmetry segment pairs

Number of S3 symmetry segment triples

C2 Segment pair 1

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

C2 Segment pair 2

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

C2 Segment pair 3

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

C2 Segment pair 4

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

C2 Segment pair 5

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

C2 Segment pair 6

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

C2 Segment pair 7

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

C2 Segment pair 8

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

C2 Segment pair 9

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

C2 Segment pair 10

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

C2 Segment pair 11

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

C3 Segment pair 1

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

C3 Segment pair 2

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

C3 Segment pair 3

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

C3 Segment pair 4

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

C3 Segment pair 5

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

C3 Segment pair 6

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

C3 Segment pair 7

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

C3 Segment pair 8

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

C3 Segment pair 9

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

C3 Segment pair 10

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

C3 Segment pair 11

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

C4 Segment pair 1

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

C4 Segment pair 2

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

C4 Segment pair 3

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

C4 Segment pair 4

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

C4 Segment pair 5

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

C4 Segment pair 6

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

C4 Segment pair 7

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

C4 Segment pair 8

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

C4 Segment pair 9

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

C4 Segment pair 10

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

C4 Segment pair 11

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

C5 Segment pair 1

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

Segment 5

1st residue

2nd residue

Segment ID

C5 Segment pair 2

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

Segment 5

1st residue

2nd residue

Segment ID

C5 Segment pair 3

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

Segment 5

1st residue

2nd residue

Segment ID

C5 Segment pair 4

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

Segment 5

1st residue

2nd residue

Segment ID

C5 Segment pair 5

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

Segment 5

1st residue

2nd residue

Segment ID

C5 Segment pair 6

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

Segment 5

1st residue

2nd residue

Segment ID

C5 Segment pair 7

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

Segment 5

1st residue

2nd residue

Segment ID

C5 Segment pair 8

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

Segment 5

1st residue

2nd residue

Segment ID

C5 Segment pair 9

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

Segment 5

1st residue

2nd residue

Segment ID

C5 Segment pair 10

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

Segment 5

1st residue

2nd residue

Segment ID

C5 Segment pair 11

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

Segment 5

1st residue

2nd residue

Segment ID

C6 Segment pair 1

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

Segment 5

1st residue

2nd residue

Segment ID

Segment 6

1st residue

2nd residue

Segment ID

C6 Segment pair 2

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

Segment 5

1st residue

2nd residue

Segment ID

Segment 6

1st residue

2nd residue

Segment ID

C6 Segment pair 3

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

Segment 5

1st residue

2nd residue

Segment ID

Segment 6

1st residue

2nd residue

Segment ID

C6 Segment pair 4

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

Segment 5

1st residue

2nd residue

Segment ID

Segment 6

1st residue

2nd residue

Segment ID

C6 Segment pair 5

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

Segment 5

1st residue

2nd residue

Segment ID

Segment 6

1st residue

2nd residue

Segment ID

C6 Segment pair 6

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

Segment 5

1st residue

2nd residue

Segment ID

Segment 6

1st residue

2nd residue

Segment ID

C6 Segment pair 7

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

Segment 5

1st residue

2nd residue

Segment ID

Segment 6

1st residue

2nd residue

Segment ID

C6 Segment pair 8

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

Segment 5

1st residue

2nd residue

Segment ID

Segment 6

1st residue

2nd residue

Segment ID

C6 Segment pair 9

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

Segment 5

1st residue

2nd residue

Segment ID

Segment 6

1st residue

2nd residue

Segment ID

C6 Segment pair 10

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

Segment 5

1st residue

2nd residue

Segment ID

Segment 6

1st residue

2nd residue

Segment ID

C6 Segment pair 11

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Segment 4

1st residue

2nd residue

Segment ID

Segment 5

1st residue

2nd residue

Segment ID

Segment 6

1st residue

2nd residue

Segment ID

S3 Segment pair 1

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

S3 Segment pair 2

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

S3 Segment pair 3

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

S3 Segment pair 4

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

S3 Segment pair 5

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

S3 Segment pair 6

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

S3 Segment pair 7

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

S3 Segment pair 8

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

S3 Segment pair 9

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

S3 Segment pair 10

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

S3 Segment pair 11

Segment 1

1st residue

2nd residue

Segment ID

Segment 2

1st residue

2nd residue

Segment ID

Segment 3

1st residue

2nd residue

Segment ID

Energy constants for unambiguous restraints

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

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

Energy constants for ambiguous restraints

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

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

Energy constants for hydrogen bond restraints

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

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

Energy constants for dihedral angle restraints

hot

cool1

cool2

cool3

Energy constants for radius-of-gyration restraints

hot

cool1

cool2

cool3

Atom selections for the radius of gyration restraint

Residual dipolar couplings 1

RDC type

SANI energy constants

First iteration

Last iteration

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_bor energy constants per stage

hot

cool1

cool2

cool3

RDC file

Residual dipolar couplings 2

RDC type

SANI energy constants

First iteration

Last iteration

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_bor energy constants per stage

hot

cool1

cool2

cool3

RDC file

Residual dipolar couplings 3

RDC type

SANI energy constants

First iteration

Last iteration

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_bor energy constants per stage

hot

cool1

cool2

cool3

RDC file

Residual dipolar couplings 4

RDC type

SANI energy constants

First iteration

Last iteration

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_bor energy constants per stage

hot

cool1

cool2

cool3

RDC file

Residual dipolar couplings 5

RDC type

SANI energy constants

First iteration

Last iteration

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_bor energy constants per stage

hot

cool1

cool2

cool3

RDC file

Residual dipolar couplings 6

RDC type

SANI energy constants

First iteration

Last iteration

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_bor energy constants per stage

hot

cool1

cool2

cool3

RDC file

Residual dipolar couplings 7

RDC type

SANI energy constants

First iteration

Last iteration

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_bor energy constants per stage

hot

cool1

cool2

cool3

RDC file

Residual dipolar couplings 8

RDC type

SANI energy constants

First iteration

Last iteration

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_bor energy constants per stage

hot

cool1

cool2

cool3

RDC file

Residual dipolar couplings 9

RDC type

SANI energy constants

First iteration

Last iteration

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_bor energy constants per stage

hot

cool1

cool2

cool3

RDC file

Residual dipolar couplings 10

RDC type

SANI energy constants

First iteration

Last iteration

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_bor energy constants per stage

hot

cool1

cool2

cool3

RDC file

Residual dipolar couplings 11

RDC type

SANI energy constants

First iteration

Last iteration

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_bor energy constants per stage

hot

cool1

cool2

cool3

RDC file

Pseudo Contact Shifts restraints

Number of PCS restraints

Tensor distance restraints file for all PCS restraints

PCS restraints 1

RDC type

PCS energy constants

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

PCS file

PCS restraints 2

RDC type

PCS energy constants

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

PCS file

PCS restraints 3

RDC type

PCS energy constants

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

PCS file

PCS restraints 4

RDC type

PCS energy constants

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

PCS file

PCS restraints 5

RDC type

PCS energy constants

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

PCS file

PCS restraints 6

RDC type

PCS energy constants

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

PCS file

PCS restraints 7

RDC type

PCS energy constants

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

PCS file

PCS restraints 8

RDC type

PCS energy constants

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

PCS file

PCS restraints 9

RDC type

PCS energy constants

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

PCS file

PCS restraints 10

RDC type

PCS energy constants

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

PCS file

PCS restraints 11

RDC type

PCS energy constants

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

PCS file

Relaxation Anisotropy restraints

Number of Anisotropy restraints

Anisotropy restraints 1

Anisotropy type

DANI energy constants

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

Correlation time

H frequency

N frequency

Anisotropy file

Anisotropy restraints 2

Anisotropy type

DANI energy constants

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

Correlation time

H frequency

N frequency

Anisotropy file

Anisotropy restraints 3

Anisotropy type

DANI energy constants

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

Correlation time

H frequency

N frequency

Anisotropy file

Anisotropy restraints 4

Anisotropy type

DANI energy constants

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

Correlation time

H frequency

N frequency

Anisotropy file

Anisotropy restraints 5

Anisotropy type

DANI energy constants

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

Correlation time

H frequency

N frequency

Anisotropy file

Anisotropy restraints 6

Anisotropy type

DANI energy constants

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

Correlation time

H frequency

N frequency

Anisotropy file

Anisotropy restraints 7

Anisotropy type

DANI energy constants

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

Correlation time

H frequency

N frequency

Anisotropy file

Anisotropy restraints 8

Anisotropy type

DANI energy constants

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

Correlation time

H frequency

N frequency

Anisotropy file

Anisotropy restraints 9

Anisotropy type

DANI energy constants

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

Correlation time

H frequency

N frequency

Anisotropy file

Anisotropy restraints 10

Anisotropy type

DANI energy constants

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

Correlation time

H frequency

N frequency

Anisotropy file

Anisotropy restraints 11

Anisotropy type

DANI energy constants

First iteration

Last iteration

Energy constants per stage

hot

cool1

cool2

cool3

Correlation time

H frequency

N frequency

Anisotropy file

Energy and interaction parameters

Nonbonded parameters

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 rigid body docking (it1)

Use constant (cdie) or distance-dependent (rdie) dielectric in it0

Use constant (cdie) or distance-dependent (rdie) dielectric in it1

Epsilon constant for the electrostatic energy term. Note that for explicit solvent refinement cdie with epsilon=1 is used.

Epsilon constant for the electrostatic energy term in it0

Epsilon constant for the electrostatic energy term in it1

Scaling of intermolecular interactions for semi-flexible SA (it1)

Initial value

Scaling of intermolecular interactions for rigid body EM

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

Esyn

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

cryoEM

cryoEM 1

cryoEM 2

cryoEM 3

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 the next 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

Rebuild missing atoms in context of the molecule partner

Perform initial rigid body minimisation

Allow translation in rigid body minimisation

it1 parameters

Initial seed for random number generator

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 interface

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 EM steps for translational minimisation?

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)

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

Use translation in loop miniwater

How many different solvation shells to generate

Analysis parameters

Full or limited analysis of results?

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

Do you want to perform advanced water analysis (increase computational time)?

COVID-19 related

HADDOCK 2.4

@Bonvinlab

HADDOCK submission

Random patches

Center of mass restraints

Surface contact restraints

Random exclusion

Radius of gyration restraint

Solvated docking mode

Cutoff for defining neighbouring flexible regions

Energy constants per stage

Energy constants per stage

Energy constants per stage

Energy constants for dihedral angle restraints

Energy constants for radius-of-gyration restraints

SANI energy constants

VEAN energy constants

SANI energy constants

VEAN energy constants

SANI energy constants

VEAN energy constants

SANI energy constants

VEAN energy constants

SANI energy constants

VEAN energy constants

SANI energy constants

VEAN energy constants

SANI energy constants

VEAN energy constants

SANI energy constants

VEAN energy constants

SANI energy constants

VEAN energy constants

SANI energy constants

VEAN energy constants

SANI energy constants

VEAN energy constants

PCS energy constants

PCS energy constants

PCS energy constants

PCS energy constants

PCS energy constants

PCS energy constants