Free Energy Perturbation (FEP)

Faster time to clinical candidate using FEP activity prediction now universally available in Flare™ V3

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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  • Given a parent ligand and protein, get accurate values for relative binding affinity within a related set of ligands
  • 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
Working with Dr Julien Michel at the University of Edinburgh UK, an expert in free energy methods, we combined and enhanced open-source tools to generate a robust, user-friendly, fully validated and accessible implementation of FEP. This enables computational chemists to predict the activities of new molecules during drug discovery, significantly reducing synthetic chemistry costs and improving the time to clinical candidate.

Mark Mackey, CSO, Cresset

I am delighted that the results from the Knowledge Transfer Partnership (KTP) / Innovate UK collaboration between my group and Cresset has been released within Flare V3. The interface designed by Cresset significantly streamlines and improves the workflow for using FEP based on open source tools developed by academic groups. This will accelerate the use of these exciting new techniques in commercial and academic laboratories worldwide.

Julien Michel, University of Edinburgh, UK


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