Free Energy Perturbation (FEP)

Given a parent ligand and protein, get accurate values for relative binding affinity within a related set of ligands

Developed in collaboration with Prof. Julien Michel at the University of Edinburgh, FEP in Flare™ combines open-source tools such as AMBER tools,  OpenMM, LOMAP, Sire and BioSimSpace with Cresset expertise in developing intuitive software to deliver an accessible and user friendly interface to a fully automated FEP workflow

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  • Seamless protein and ligand setup in GUI
  • Generate your ligand starting poses by aligning them to the parent ligand using Flare’s alignment feature, or dock them into the protein associated with your FEP project
  • Automatically generate the perturbation network with options to refine the map to ensure it is exactly as you want
  • Configure your calculation to enhance your results (simulation time and number of λ windows)
  • Optimize your calculation time by using the Cresset Engine Broker to connect to a local cluster or cloud computing facilities
  • View all aspects of your FEP calculation results in a dedicated window and identify problematic transformations
  • Fully validated against literature benchmarks


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