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 Databases named ‘brood-database-chembl-xxx.tar.gz’ are available in organizational data, where xxx is a version number.

Promoted Parameters

Title in user interface (promoted name)

Inputs

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

  • Required

  • Type: fragment_input

Fragment Database file (db_file_field): Brood fragment database, from which fragments and scaffold couplings to be derived

  • Required

  • Type: file_in

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

  • Type: data_source

Outputs

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 dataset of brood query

  • Required

  • Type: dataset_out

  • Default: Output for BROOD - 3D query

Output Dataset (out): Output dataset of successful calculations

  • Required

  • Type: dataset_out

  • Default: Output for BROOD - 3D Fragment Replacement