Free Energy Perturbation (FEP)

Use Flare FEP to refine your docking results, make the right structure-based design choices and enable lead optimization with confidence

Robust and efficient calculations

  • Seamlessly set up proteins and ligands
  • Align ligand poses easily using the ligand alignment component of Flare, or dock ligands to the protein associated with your Flare FEP project
  • Use the automated process to create an efficient perturbation network, with options to refine the map
  • Easily view and troubleshoot all aspects of your Flare FEP calculation results in a dedicated window and identify problematic transformations
  • View, sort and prioritize your ligands using their predicted activity

Accurate FEP calculations

  • Accurately calculate the relative binding free energy of a closely related (or congeneric) series of ligands (Assessment of Binding Affinity via Alchemical Free-Energy Calculations J. Chem. Inf. Model. 2020, 60, 6, 3120–3130)
  • Precision is obtained in your Flare FEP calculations using fully connected, two-way networks, which enable more accurate error estimation for each link and thorough analysis of cycle errors
  • Easily generate network graphs by adding automated intermediates to better link structurally related ligands

Request recording of webinar ‘FEP methods in Flare V5: New features and enhancements’

Free energy cycle

Free energy cycle

Faster FEP calculations

  • Split your Flare FEP calculations into the optimal package size for your GPU resources, enabling single compounds to be predicted in as little as 30 minutes
  • Flare FEP uses an advanced integrator, including hydrogen mass repartitioning and a more optimal water box shape and size for the simulation
  • Optimize calculation time by using the Cresset Engine Broker™ to connect to a local cluster or cloud computing facilities
  • Achieve a more tailored, and quicker, simulation as assignment of the number of λ windows to use between each perturbation is determined by the software adaptively and automatically

Flare V5 FEP speedup overV4

Flare FEP calculations are 2-3.5 times faster in Flare V5 compared to Flare V4

Flare FEP resources


Explore further to see how Flare can add fresh insights into your structure-based design

Explore further