Promising results for three GPCR benchmarks using Flare™ FEP for accurate binding affinity calculations in membrane proteins

Free Energy Perturbation for membrane proteins

Free Energy Perturbation (FEP) has a well-earned reputation as an incredibly reliable and accurate method for calculating binding free energies (binding affinities) of small molecule ligands in protein complexes. In soluble proteins, a scientist can expect a predicted affinity with an accuracy within 1 kcal/mol to the measured experimental affinity. Of course, however, membrane proteins pose more difficulty and introduce more error into the usually very robust method. Some such challenges and errors come from: uncertainty in atomic positions, binding pose, water placements and in vivo conformation of the ligand (membrane) - complex.

A recent study of 3 GPCR benchmark targets using Flare FEP is compared to the results of a study by Ross, G. et al.1 (Table 1). These results indicate that Flare FEP can be used to accurately predict binding affinities with a prediction error within 1.17- 0.66 kcal/mol and with low linkwise RMSD. The results presented from Flare FEP implement an 'out of the box' approach: after careful system preparation using Flare tools, the Flare FEP calculations were run using the default options (including the automated addition of intermediates) without extra troubleshooting post-calculation.

3 GPCR benchmarks: results

Table 1. Comparing reported results from a study by Ross, G. et al.1 with Flare FEP results for the 3 GPCR benchmarks. Dashed lines indicate where equivalent statistical results for comparison are not available.  

Target Approach R2 MUE Tau LinkwiseRMSD No. of Ligands No. of Perturbations
A2A Ross, G. et al.1 0.50 - - 1.22 17 28
Flare FEP 0.55 0.66 0.54 0.95 17 42
OX2 Ross, G. et al.1 0.33 - - 1.43 51 103
Flare FEP 0.53 0.71 0.56 1.23 55 162
P2Y1 Ross, G. et al.1 0.48 - - 1.42 30 76
Flare FEP 0.57 1.17 0.56 1.65 31 90


Table 1 compares data published by Ross et al1. versus recent results obtained using Flare FEP for the same 3 GPCR benchmark targets, A2A, OX2 and P2Y1. The results show that Flare FEP achieves a state-of-the-art performance on these systems, further validating its suitability for use on even challenging membrane-bound proteins. This is exciting in terms of drug discovery potential in the very large and important domain of membrane proteins.

Please see the case study: Free Energy Perturbations (FEP) on membrane targets: capturing lipid exposed binding in the P2Y1 GPCR complex and webinar Calculating ligand binding affinities at the lipid /membrane interface P2Y1 GPCR complex for more detail on the workflow used in the example P2Y1. For any queries, comments and suggestions on this work please do not hesitate to Contact us.

For more information on how Free Energy Perturbation can accelerate drug discovery with computational prediction of molecular binding affinities watch our recent webinar.


  1. Ross, G. et al. The maximal and current accuracy of rigorous protein-ligand binding free energy calculations, Communications Chemistry, 2023, doi: 10.1038/s42004-023-01019-9.

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