Water replacement

Pick up additional ligand-protein interactions displacing crystallographic waters

Displacing crystallographic water molecules with Spark

Water molecules situated within the protein active site can either mediate or impair the interaction between a ligand and a protein. In situations where water stability analysis detects an unstable water molecule, Spark enables users to grow a ligand into the space that the water molecule is occupying, to displace the water and enable a more favorable protein-ligand interaction, using a simple workflow.

  • Bring together the 3D structures of your starting reference molecule and the crystallographic water you want to displace
  • Define the region of the starter molecule to be grown
  • Mimic the water electrostatics constraining the water fields
  • Customize your fragment search by selecting the database and fragment types better suiting your design needs
Read case study: 'Displacing crystallographic water molecules with Spark'

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