tbl configuration file

Restraints are very powerful tools to guide the docking process, to use its full potential, in haddock-restraints we use a configuration file to define the restraints. This file is a JSON file that contains the information needed to generate the restraints.

To use the full potential of ambiguous restraints we have introduced the concept of interactors, which are arbitrary groups of residues that can be used to define the restraints.

haddock-restraints supports an unlimited number of interactors, and each interactor can have an unlimited number of residues. This allows you to define complex restraints that can be used to guide the docking process.

• Mandatory fields
• Optional fields
• Reference guide with detailed explanation of the fields in the configuration file

Mandatory fields

• id: an integer that identifies the interactor
• chain: the chain of the interactor
• active: a list of residues that are active in the interaction
• passive: a list of residues that are passive in the interaction
• target: a list of integers that identifies the interactors that the current interactor interacts with

A minimal configuration file would look like this:

[
  {
    "id": 1,
    "chain": "A",
    "active": [950],
    "passive": [],
    "target": [2]
  },
  {
    "id": 2,
    "chain": "B",
    "active": [41, 42, 43, 44, 45],
    "passive": [],
    "target": [1]
  }
]

Optional fields

• structure: the PDB file that contains the structure of the interactor
• passive_from_active: if true, the passive residues are defined based on the active residues (requires structure)
• surface_as_passive: if true, the passive residues are defined based on the surface accessibility of the residues (requires structure)
• filter_buried: if true, the buried residues are filtered out (requires structure)
• filter_buried_cutoff: the cutoff to consider a residue as buried, default = 0.7 (requires structure)
• target_distance: the distance to consider two residues as interacting, default = 2.0 (see Note)
• lower_margin: the lower bound correction subtracted from the target_distance to define the lower distance boundary.
• upper_margin: the upper bound correction added to the target_distance to define the upper distance boundary.
• active_atoms: a list containing which active atoms should be included in the restraint; if not defined all atoms are included automatically
• passive_atoms: a list containing which passive atoms should be included in the restraint; if not defined all atoms are included automatically

Note: Check this paper for a deeper explanation about the target distance and the margins. The default value of 2.0Å (which might seem short) is used because of the way the effective distance is calculated from all pairwise combinations of atom it will always be shorter than the shortest distance measured.

A configuration file with optional fields would look like this:

[
  {
    "id": 1,
    "chain": "A",
    "active": [934, 939],
    "passive": [],
    "structure": "2oob.pdb",
    "target": [2],
    "passive_from_active": true,
    "filter_buried": true
  },
  {
    "id": 2,
    "chain": "B",
    "active": [68],
    "passive": [],
    "target": [1]
  },
  {
    "id": 3,
    "chain": "B",
    "active": [],
    "passive": [],
    "target": [1],
    "structure": "2oob.pdb",
    "surface_as_passive": true
  }
]

Reference guide

• id

  • type: integer
  • description: an integer that identifies the interactor

• chain

  • type: string
  • description: the chain of the interactor

• active

  • type: list of integers
  • description: a list of residues that are active in the interaction

• passive

  • type: list of integers
  • description: a list of residues that are passive in the interaction

• target

  • type: list of integers
  • description: a list of integers that identifies the interactors that the current interactor interacts with

Optional fields are:

• structure

  • type: string
  • description: the PDB file that contains the structure of the interactor. If using relative paths, they should be relative to the configuration file

• passive_from_active

  • type: boolean
  • description: define passive residues are defined based on the active residues
  • requires: structure

• surface_as_passive

  • type: boolean
  • description: define passive residues are defined based on the surface accessibility of the residues
  • requires: structure

• filter_buried

  • type: boolean
  • description: filter out buried residues
  • requires: structure

• filter_buried_cutoff

  • type: float
  • description: the cutoff to consider a residue as buried, default = 0.7
  • requires: structure

• target_distance

  • type: float
  • description: the distance to consider two residues as interacting, default = 2.0

• lower_margin

  • type: float
  • description: the lower bound correction subtracted from the target_distance to define the lower distance boundary

• upper_margin

  • type: float
  • description: the upper bound correction added to the target_distance to define the upper distance boundary