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Site Map or Scaffold Placement 

After selecting a binding site, the next step is positioning initial fragments within it. This can be done using one of two modules:

  1. Site Map – Suitable for users without specific chemotype preferences.

  2. Scaffold Placement – Recommended for users who have a preferred molecular core.


The Site Map module allows the placement of triatomic fragments that commonly participate in hydrogen bonding.

  • Ideal for cases where the exact scaffold structure is unknown.
  • Helps in exploring possible interactions between fragments and the protein.
  • Provides a diverse set of potential fragments to guide scaffold design.

The Scaffold Placement module is used to dock a user-defined scaffold into the binding pocket.

  • Recommended when you already have a preferred molecular core based on synthetic accessibility or prior knowledge.
  • Ensures that key functional groups are correctly positioned to interact with the binding site.

Each module serves each own purpose, depending on whether you want to explore possible binding interactions (Site Map) or find appropriate binding mode for a predefined scaffold (Scaffold Placement).