BROOD - Query Builder
Description
BROOD - Query Generator is a tool for creating one or more BROOD queries, 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.
Provide a lead molecule through the Query Sketcher and choose one of three selection modes. The floe builds the appropriate BROOD query (or queries) from the atoms you select:
Select atoms to replace (classic brood query) - select the fragment to be replaced. This produces a single query for fragment replacement.
Select atoms for linking/cyclization - select two segments to be linked. This produces a single cyclization/linking query.
Select atoms to keep (automatic query generation) - select the portion of the molecule to preserve. BROOD automatically enumerates candidate fragments to replace, producing multiple queries.
An optional Design Unit dataset can be supplied to define the protein context used when building the query. The resulting query (or queries) are written to the output dataset.
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