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