3D QSAR Model: Validation

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Models

Description

The 3D QSAR Model: Validation Floe is a tool for performing validation of a model against an external dataset.

The model validation floe requires two datasets: (1) a dataset of a model with stored receptors and reference molecules, if any, obtained from using the 3D QSAR Model: Builder Floe and (2) a dataset of test set molecules, along with their experimental potency.

Outputs from this floe contain a validation report and an output dataset with model predictions, along with 3D conformers.

Promoted Parameters

Title in user interface (promoted name)

Inputs

Ligand Database (in): Dataset with external molecules for validation.

  • Required

  • Type: data_source

Model (model): Dataset containing the model.

  • Required

  • Type: data_source

Potency Parameters

Input Potency field (in_potency_field): Field containing input potency data

  • Required

  • Type: field_parameter::float

  • Default: potency

Unit for Potency (potency_unit): Unit for input potency field (e.g. nanomolar or micromolar for IC50 and log for pIC50)

  • Type: string

  • Default: log

  • Choices: [‘micromolar’, ‘nanomolar’, ‘log’]

Minimum Potency (potency_min): Molecules with potency (log unit) at or below this value are not trustworthy and discarded.

  • Type: decimal

  • Default: 0.0

Maximum Potency (potency_max): Molecules with potency (log unit) at or above this value are not trustworthy and discarded.

  • Type: decimal

  • Default: 15.0

3D Conformer Parameters

Use Input 3D (use_input_3d): Whether to use 3D input structures. Flag will be ignored for molecules without 3D input structures.

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Charge Method Parameters

Charge Type (method_type): Charge assignment method.

  • Type: string

  • Default: am1bcc

  • Choices: [‘am1bcc’, ‘mmff’, ‘current_charges’]