BROOD - 3D Fragment Replacement

Category Paths

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

  • Product-based/BROOD

  • Role-based/Computational Chemist

  • Solution-based/Virtual-screening/DB Search

  • Task-based/Scaffold-Hopping

  • Role-based/Medicinal Chemist

Description

BROOD - 3D Fragment Replacement is a lead generation tool designed to generate new and diverse compounds that satisfy isosteric and chemical feature constraints while also incorporating synthetic feasibility. Starting with a hit or lead molecule, BROOD generates bioisosteric analogs by replacing user-specified portions of the lead with fragments that have similar shape and electrostatics, but with potentially novel connectivity and chemistry. Fragments and scaffold couplings are derived within the scope of a known chemical space, based on the specified Brood Fragments Database.

The default Brood Fragments Database Collection named ‘brood-database-chembl-xxx’ is available in organizational data, where xxx is a version number.

Promoted Parameters

Title in user interface (promoted name)

Input parameters

Query Input (ui_result): Must be a molecule with valid 3D coordinates

  • Type: fragment_input

Input Collections (collection): Input database collection

  • Required

  • Type: collection_source

Input Protein (protein): Optional dataset containing Protein molecule or Design Unit

  • Type: data_source

Output parameters

Save Input Query (save_input_query): This flag specifies whether the input query should be saved

  • Required

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Query output (data_out): Output for BROOD - 3D query

  • Required

  • Type: dataset_out

  • Default: Output - brood query

Output Dataset (out): Output dataset of successful calculations

  • Required

  • Type: dataset_out

  • Default: Output for BROOD - 3D Fragment Replacement

Failed Dataset (failed): Output dataset of failed calculations.

  • Required

  • Type: dataset_out

  • Default: Failed Output for BROOD - 3D Fragment Replacement

Brood settings

Generate Brood clusters report (create_report): Whether or not to generate Brood clusters report

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

ET mode (ET): Boolean flag indicating whether or not to use ET mode

  • Type: boolean

  • Default: False

  • Choices: [True, False]

linkOnly mode (linkOnly): Boolean flag indicating whether or not to use linkOnly mode

  • Type: boolean

  • Default: False

  • Choices: [True, False]