Binding Free Energy Estimator 3

Release:: 3.2.1
Date:: May 02, 2026

Binding Free Energy Estimator (BFEE) is a Python-based software package that automates absolute binding free-energy calculations through alchemical and geometrical routes using molecular dynamics simulations.

Theoretical Background

The degrees of freedom of the protein-ligand or host-guest system are described by a series of geometric variables, or collective variables, as first described by the Karplus group. In BFEE, generalized best-fit-rotation-based geometric variables are used, making the method in principle applicable to any protein-ligand complex. See this paper for an introduction to these variables.

In the geometric route, the degrees of freedom are investigated one by one through one-dimensional free-energy calculations. BFEE supports WTM-eABF and plain eABF for these calculations. The alchemical route is a variant of the double decoupling method (DDM). It uses a thermodynamic cycle in which the ligand and geometric restraints are decoupled independently to improve simulation convergence.

Recent BFEE3 releases also include high-efficiency methods such as Lucid DDM (LDDM) and WTM-lambdaABF, plus a streamlined geometrical route for protein-protein binding free-energy calculations.

Features

Generate input files for absolute binding free-energy calculations.
Support protein-protein and protein-ligand complexes.
Support NAMD for alchemical and geometrical routes, and GROMACS for the geometrical route.
Support PSF/PDB/PRM, PRM7/RST7, and TOP/PDB input systems.
Support DDM, LDDM, WTM-eABF, WTM-lambdaABF, and GaWTM-eABF workflows.
Provide quick setup actions for common calculation types.
Provide an OpenAI-compatible AI assistant for setup guidance.
Perform post-treatment and quick plotting inside the GUI.

Requirements

Python 3.6+
PySide6, appdirs, MDAnalysis, matplotlib, numpy<2.3, scipy, parmed, requests
NAMD 3.0 or later
GROMACS 2024 or later

Since both NAMD and GROMACS include Colvars in their recent binaries, each BFEE3 release corresponds to a specific tested NAMD/GROMACS version. Use the matching or a later MD engine version for free-energy calculations.

Installation

We suggest installing BFEE through conda in a new environment.

conda create --name bfee   (optional)
conda activate bfee        (optional)
conda install -c conda-forge BFEE2

Please force numpy<2.3 if your environment pulls a newer NumPy release, because recent NumPy versions can break ParmEd compatibility.

Usage

Run BFEE2Gui.py in a terminal or PowerShell. On Microsoft Windows, you may need to use the absolute path.

Citations

BFEE main protocol: Fu et al. Nat. Protoc. 2022, 17, 1114-1141
BFEE2: Fu et al. J. Chem. Inf. Model. 2021, 61, 2116-2123
Protein-protein BFEE: Fu et al. J. Chem. Inf. Model. 2023, 63, 2512-2519
LDDM route: Bian et al. Nat. Comput. Sci. 2025, 5, 621-626
WTM-lambdaABF: Zhou et al. Acc. Chem. Res. 2026, 59, 90-102
Alchemical and geometrical routes: Gumbart et al. J. Chem. Theory Comput. 2013, 9, 794-802
WTM-eABF: Fu et al. Acc. Chem. Res. 2019, 52, 3254-3264 and Fu et al. J. Phys. Chem. Lett. 2018, 9, 4738-4745
Collective variables: Fu et al. J. Chem. Theory Comput. 2017, 13, 5173-5178

Contact Us

This software is distributed under the GPLv3 license. For more information about BFEE, contact Haohao Fu (fhh2626@nankai.edu.cn) and Haochuan Chen (yjcoshc@mail.nankai.edu.cn).