3D Scaffold Hopping. Guaranteed.


  • Replace central elements in known bioactive molecules
  • Generate new scaffolds in 3D in the blink of an eye
  • Impose pharmacophore constraints interactively
  • Custom design your own fragment database for scaffold replacement


  • In my opinion, software of this sort belongs on the desktop of any chemist designing bioactive molecules.
    John van Drie in JACS 131 (2009) 1617
  • ReCore works well! It has a user-friendly interface, and the constraints are easy to set up.
    GSK, China.
  • The diversity of solutions from ReCore is much better than similar types of software.
    Roberto Forlani, NiKem Research Srl, Italy.
  • ReCore proposed an elegant ring closure in a linear scaffold, not only retaining key pharmacophore features, but activity as well.
    Sander Nabuurs, LeadPharma, The Netherlands.

scientific background

  • ReCore replaces a given core: Given a pre-defined central unit of a molecule (the core), fragments are searched in a 3D database for the best possible replacement – whilst keeping all connected residues, i.e., the rest of the query compound in place. Additionally, user-defined "pharmacophore" constraints can be employed to restrict solutions.
  • A typical workflow is a two stage process, of which Stage A needs to be performed only once (click picture for further information).
  • For more details please see the original publication:

    Maass, P.; Schulz-Gasch, T.; Stahl, M.; Rarey, M; ReCore: A Fast and Versatile Method for Scaffold Hopping Based on Small Molecule Crystal Structure Conformations. J. Chem. Inf. Model. 2007

what's new?

ReCore is now part of LeadIT.


ReCore has been developed by Patrick Maass in Matthias Rarey's group at the ZBH, University of Hamburg, in collaboration with F. Hoffmann-La Roche AG (Basel, Switzerland).

The graphics were made available by courtesy of Martin Stahl and Tanja Schulz-Gasch at F. Hoffmann-La Roche.

additional material

ReCore requires a 3D fragment space to search in. The evaluation copy comes with a small sample space. We recommend you to download either:

[1]All ReCore spaces need to be de-compressed in two steps. Please unzip the download, and check instructions in the readme.
[2]The CSD ReCore index requires a license from CCDC.
[3] The GDB17-based index was created with help and friendly permission from Prof. Jean-Louis Reymond. Note that any publication about it must refer to the original authors (cp. Readme in the package). Further note that this index contains virtual molecules made to provide food for thought. They are laden with fluorine atoms which you may want to eliminate in a post-processing!


stay tuned with all the breaking news.


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