Generate highly innovative ideas for your project to explore chemical space and escape IP and toxicity traps


Find biologically equivalent replacements for key moieties in your molecule and be guided through the process of growing and linking ligands

Whether your research goal is R-group exploration, patent busting or scaffold hopping, your results will include structures you have thought of yourself, plus new structures that make chemical sense and are totally unexpected

Spark gives you a head start, letting you explore the likely results of your substitutions from the desktop before transferring your best ideas to the bench

  • Generate highly innovative ideas for your project
  • Move to new series and non-obvious IP by swapping scaffolds
  • Find the best R-groups from your reagents
  • Grow a ligand into new space, picking ligand-protein interactions directly from the active site, or guided by existing ligands

  • Join two ligands sitting in different regions of your protein active site
  • Cyclize a molecule by joining two atoms with a linker
  • Search for an R-group which will displace a crystallographic water molecule near your ligand

Request recording of webinar 'Escape prior art: Find accessible new chemical matter for your project'

Spark databases

Spark databases are derived from commercially available screening compounds (eMolecules screening compounds), literature reports (ChEMBL), theoretical ring systems (VEHICLe) and commercial reagents (eMolecules building blocks).

Larger databases are split based on the frequency of occurrence of the fragments.

Spark databases based on small molecule crystal structure data from the Crystallography Open Database and Cambridge Structural Database are also available.

find out more about spark databases

Docking in Spark

Find fragments picking ligand-protein interactions directly from the protein active site. Use this method to grow ligands and fragments into unoccupied pockets of the target protein, and whenever you wish to find novel results making interactions with the active site of your protein not mapped by an existing starter or reference molecule.

Right: Docking workflow in Spark (PDB: 6TCU). A) A portion of the starter molecule is selected for replacement. B) The selected fragment is deleted. C) A new fragment is attached in a sensible orientation to the truncated starter molecule. D) The pose of the new result molecule is optimized using Lead Finder™.

Easy to use interface

  • Quickly generate a range of novel molecules from an initial structure
  • Profiling and scoring help you choose the most innovative and tractable leads with the properties you need
  • Use filters to find the result with the right mix of physicochemical properties and biological activity
  • Visualize results in detail side-by-side, or cluster similar chemical scaffolds
  • Search for moieties from real, published or unexplored compound databases
  • Create your own custom databases based on the reagents you have available or your proprietary chemistry

Customers say Spark is the best scaffold hopping software they have ever used

Spark works in electrostatic and shape space so it can match the nature of your molecules better than any other tool. When you grow ligands into new space, or link ligands from different regions of your protein active site, Spark gives you complete control. You can choose to be guided by your knowledge of existing ligands, your reagent availability, or by the ideal property profile.

Licensing Spark

Try Spark on your project

See flexible licensing options