BROOD - 3D Fragment Similarity¶
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 - Fragments Similarity aligns and scores a database of fragments to a template fragment. The alignments can be used for a variety of purposes. The scores are used to rank fragments based on the probability that they share relevant (biological) properties with the query fragment.
Fragments are aligned based on their shape similarity and their distributions of chemical features, as desired. The minimal inputs is a query fragment with a single 3D conformation, and a search database of fragments with multiple 3D conformations.
Output from the floe is a hitlist with highly similar fragments at the top. Additional output data columns consist of individual similarity scores.
Promoted Parameters
Title in user interface (promoted name)
Brood settings
Num Best Hits (best_hits): Number of best-scoring fragments to keep
Required
Type: integer
Default: 500
Score type (score_type): Score type to be used for Overlay
Type: string
Default: rocs
Choices: [‘rocs’, ‘ET’, ‘LinkOnly’]
Ring Requirement (ring_only): Ring requirement between attachment points in fragment.-2: Ring of any size; -1: Exclude rings; 0: Ring agnostic,1-12: Ring of specified size
Type: integer
Default: 0
Charge type (charge_type): Charge type to be used for Overlay
Type: string
Default: mmff94
Choices: [‘mmff94’, ‘fileChrg’]