A typical workflow is a two stage process, of which Stage A needs to be performed only once:
||Stage A: "Processing Phase" / Database and Index Generation
- Decompose 3D ligand data (such as the CSD) based on user-defined subgraph ("shredding") rules
- Rule out unwanted fragments based on filters (user-definable)
- Create a 3D-database index for efficient access
||Stage B: "Query Execution"
- Define a query by selecting bonds that separate "Core" and "Substituents"; i.e., the scaffold from the attached residues
- Define ligand-based pharmacophore constraints like H-bond acceptors, donors etc.; also exclusion volumes are supported
- Retrieve geometrically suitable new scaffolds at lightning speed by scanning the database with ReCore
- Visually inspect and cherry pick the fragments from a rank sorted list.
- Output the selection in mol2 format for further processing.