Papers › Using the Fast Fourier Transform in Binding Free Energy Calculations
Using the Fast Fourier Transform in Binding Free Energy Calculations
Trung Hai Nguyen, Huan-Xiang Zhou, David D. L. Minh
According to implicit ligand theory, the standard binding free energy is an exponential average of the binding potential of mean force (BPMF), an exponential average of the interaction energy between the ligand apo ensemble and a rigid receptor. Here, we use the Fast Fourier Transform (FFT) to efficiently estimate BPMFs by calculating interaction energies as rigid ligand configurations from the apo ensemble are discretely translated across rigid receptor conformations. Results for standard binding free energies between T4 lysozyme and 141 small organic molecules are in good agreement with previous alchemical calculations based on (1) a flexible complex (R ~ 0.9 for 24 systems) and (2) flexible ligand with multiple rigid receptor configurations (R ~ 0.8 for 141 systems). While the FFT is routinely used for molecular docking, to our knowledge this is the first time that the algorithm has been used for rigorous binding free energy calculations.
In Syntology Open this paper in Syntology's Atlas, the map of the papers in Syntology's graph and their citations.
Code
Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.
Code Syntology ran Syntology
Not run by Syntology. Nothing on this page verifies that the listed code works.
Tasks
Results from the paper archive 2025-07-28
No leaderboard rows for this paper in the archive.
Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections