ReCore: a typical workflow

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
  1. Decompose 3D ligand data (such as the CSD) based on user-defined subgraph ("shredding") rules
  2. Rule out unwanted fragments based on filters (user-definable)
  3. Create a 3D-database index for efficient access
Stage B: "Query Execution"
  1. Define a query by selecting bonds that separate "Core" and "Substituents"; i.e., the scaffold from the attached residues
  2. Define ligand-based pharmacophore constraints like H-bond acceptors, donors etc.; also exclusion volumes are supported
  3. Retrieve geometrically suitable new scaffolds at lightning speed by scanning the database with ReCore
  4. Visually inspect and cherry pick the fragments from a rank sorted list.
  5. Output the selection in mol2 format for further processing.

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