Molecular docking models data formats

Required data tables:
  • Molecular docking models, to identify models for a specified effect (receptor)

  • Molecular docking binding energies, to specify the binding energies per substance for the receptor

Molecular docking models

Contains definitions of molecular docking models for a given effect (molecular initiating event), for example parameters needed in the conversion of binding energies to group memberships or to relative potency factors. Substance specific binding energies are specified in the binding energies table.

Molecular docking models

Each docking model has a unique identifier, and optionally a name and a description. Each model is linked to an effect using the idEffect field and optionally a binding threshold and the number of receptors can be added. A reference to the source of the data can be stored in the reference field.

Table aliases: MolecularDockingModels, MolecularDockingModel, BindingEnergyModels, BindingEnergyModel.

Table 163 Table definition for MolecularDockingModels.
Name Type Description Aliases Required

id

AlphaNumeric(50)

The unique identification code of the molecular docking model.

idMolecularDockingModel, idBindingEnergyModel

Yes

Name

AlphaNumeric(100)

The name of the molecular docking model.

Name

No

Description

AlphaNumeric(200)

Description of the molecular docking model.

Description

No

idEffect

AlphaNumeric(50)

The effect code, typically for the Molecular Initiating Event that is modelled

idEffect, EffectId, Effect

Yes

Threshold

Numeric

Threshold Molecular Docking binding energy (group membership = 1 when higher).

No

NumberOfReceptors

Integer

Example parameter needed for translating Molecular Docking binding energies to RPFs.

No

Reference

AlphaNumeric(200)

External reference(s) to sources containing more information about the molecular docking model.

References

No

Molecular docking binding energies

Molecular docking model binding energies per substance

Table aliases: MolecularBindingEnergies, MolecularBindingEnergy, BindingEnergies, BindingEnergy, MolecularDockingBindingEnergies, MolecularDockingBindingEnergy.

Table 164 Table definition for MolecularBindingEnergies.
Name Type Description Aliases Required

idMolecularDockingModel

AlphaNumeric(50)

The id of the molecular docking model or source.

idMolecularDocking, MolecularDockingModel

No

idSubstance

AlphaNumeric(50)

The code of the substance.

idSubstance, SubstanceId, SubstanceCode, Substance

Yes

BindingEnergy

Numeric

Molecular Docking binding energy.

MolecularDockingBindingEnergy

Yes