3D QSAR Model: Builder¶
Category Paths
Follow one of these paths in the Orion user interface, to find the floe.
Models
Description
The 3D QSAR Model: Builder Floe is a tool for building models with 3D descriptors. The floe incorporates: (1) 3D conformer generation and charge assignment; (2) hyperparameter optimization for ROCS- and EON-based kernel-PLS model building; (3) cross-validation; (4) model building; and (5) optional external validation.
Building models using this floe requires one or two datasets based on a specific usage scenario: (1) a dataset of molecules along with their potency without a tagged external validation set and (2) an optional dataset of pre-aligned receptors for Posit pose generation or reference molecules for FlexiROCS conformer generation.
Outputs from this floe contain: (1) a model dataset; (2) a training set conformer dataset used for model building (optional); and (3) an external validation dataset (optional).
The output model dataset stores the receptors or reference molecules provided, which will be read in the 3D QSAR Model: Validation and 3D QSAR Model: Predictor Floes.
The floe also produces hyperparameters optimization, cross-validation, and (optionally) the external validation reports.
Note: If the training set is relatively large (e.g., greater than 100), the leave-one-out cross-validation is not necessary and can slow down the floe. Consider switching to random for split method under the “Cross Validation Parameters” section, in such cases.
Promoted Parameters
Title in user interface (promoted name)
Cross Validation Parameters
Split Method (split_method): Way to split the dataset into training and validation set
Type: string
Default: leave one out
Choices: [‘random’, ‘leave one out’]
Percentage (Random Split) (percentage): The percentage of records used for training in random split
Type: decimal
Default: 90.0
Number of Split Sets (Random Split) (num_random_set): Number of times the random split to perform
Type: integer
Default: 50
External Validation Parameters
Do External Validation (do_ext_valid): Whether to do external validation. If true, floe will look for specified tag field with specified tag value to identify external validation set.
Type: boolean
Default: False
Choices: [True, False]
External Validation Tag Field (in_test_tag_field): Field containing tag for external validation set
Type: field_parameter::int
Default: External validation tag
External Validation Set Tag Value (test_tag_value): Value of tag field for external validation set
Type: integer
Default: 1
Inputs
Ligand Database (in): Dataset containing the ligand molecules to process.
Required
Type: data_source
Receptors/Reference Molecules (receptors): Dataset containing pre-aligned receptors/reference molecules.
Type: data_source
Outputs
Output Model Dataset (out): Output dataset containing built models and receptors/reference molecules.
Required
Type: dataset_out
Default: Output for 3D QSAR Model: Builder
Failed Dataset (failed): Output dataset of failed calculations.
Required
Type: dataset_out
Default: Failed Output for 3D QSAR Model: Builder
Training Conformer Output Dataset (train_pose_out): Optional output dataset containing training set conformers if Output Training Conformers is On.
Required
Type: dataset_out
Default: Training Conformer Output
External Validation Output Dataset (ext_valid_out): Optional output dataset containing external validation results if Do External Validation is On.
Required
Type: dataset_out
Default: External Validation Output
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]
Output Training Conformers (output_train_pose): Whether to output training set conformers used for model building.
Required
Type: boolean
Default: False
Choices: [True, False]
Charge Method Parameters
Charge Type (method_type): Charge assignment method.
Type: string
Default: am1bcc
Choices: [‘am1bcc’, ‘mmff’, ‘current_charges’]
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