BROOD - Query Builder

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 - Query Generator is a tool for creating a Brood Query, that can be used with the BROOD - 3D Fragment Replacement floe to generate bioisosteric analogs by replacing specified portions of the Query with fragments that have similar shape and electrostatics, but with potentially novel connectivity and chemistry.

Promoted Parameters

Title in user interface (promoted name)

Inputs

Query Sketcher (ui_result): (Optional) Dataset containing 3D molecule

  • Required

  • Type: fragment_input

Design Unit (data_in): (Optional) Dataset containing design unit

  • Type: data_source

Components to keep as the ‘protein’ (protein_mask): DU components to use as the ‘protein’.

  • Type: string

  • Default: [‘protein’, ‘nucleic’, ‘cofactors’, ‘other_ligands’, ‘other_cofactors’]

  • Choices: [‘protein’, ‘nucleic’, ‘ligand’, ‘solvent’, ‘metals’, ‘counter_ions’, ‘lipids’, ‘packing_residues’, ‘sugars’, ‘undefined’, ‘cofactors’, ‘excipients’, ‘polymers’, ‘post_translational’, ‘other_proteins’, ‘other_nucleics’, ‘other_ligands’, ‘other_cofactors’]

Outputs

Query output (data_out): Output dataset containing BROOD query

  • Required

  • Type: dataset_out

  • Default: Output BROOD query