Spark™
Water replacement
Pick up additional ligand-protein interactions displacing crystallographic waters
Uploading the protein-ligand complex into Spark for the water replacement experiment.
Thanks to its easy-to-follow wizard, Spark users can set up and run their water replacement experiments, through a series of simple clicks.
Select the water molecule that you want to replace within the protein active site.
Selecting the region of the starter molecule to replace as part of the Spark water replacement experiment.
Setting the field constraints to the negative and positive field points of the water molecule.
Selecting which fragment databases will be searched as part of the Spark water replacement experiment.
Visualization of results from the water replacement experiment in Spark.
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
Uploading the protein-ligand complex into Spark for the water replacement experiment.
Thanks to its easy-to-follow wizard, Spark users can set up and run their water replacement experiments, through a series of simple clicks.
Select the water molecule that you want to replace within the protein active site.
Selecting the region of the starter molecule to replace as part of the Spark water replacement experiment.
Setting the field constraints to the negative and positive field points of the water molecule.
Selecting which fragment databases will be searched as part of the Spark water replacement experiment.
Visualization of results from the water replacement experiment in Spark.