Ligand growing and docking

Pick additional interactions from the active site of your protein with Spark ligand growing experiments

Grow ligands into new spaces, guided by an existing ligand or fragment

With Spark’s ‘Ligand Growing’ experiment you can grow your starter molecule to pick additional interactions with the active site of your protein and increase its binding affinity, guided by existing ligands or fragments mapping a different region of the same active site.

  • Load the starter molecule into Spark, in its bioactive conformation
  • Load additional ligand(s) to guide the growth of your starter molecule
  • Select which fragment collections will be searched from a wide range of available databases
  • Optionally customize your Spark search by applying physico-chemical and structural filters during the search
Read case study: 'Using Spark reagent databases to find the next move'

Grow your ligands into unexplored parts of your protein's active site

In cases where no ligand is available to guide the growth process, Spark ‘Docking’ experiments enable you to grow your ligands into unoccupied parts of the protein active site, picking new ligand-protein interactions directly from the active site.

The 'Docking' method in Spark uses the Lead Finder™ algorithm to calculate a docking score for each binding pose and prioritize the best result molecules.

  • Select a region of the starter molecule to replace or to grow from, and remove these atoms
  • Load a prepared version of the protein to be used in the Spark docking experiment
  • Find new suitable fragments to place in a sensible orientation within the active site of the protein, guided by Cresset’s unique XED force field model of electrostatics
Read case study: 'Pick new ligand-protein interactions from the active site with Spark'

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