BFEE2

BFEE2 performs absolute binding free-energy calculations for protein–ligand and host–guest systems using alchemical transformations and geometric approaches implemented with molecular dynamics.

Key Features:

• Implementation: Python-based automation of absolute binding free-energy calculations.
• Supported methods: Alchemical transformations and geometric approaches executed via molecular dynamics simulations.
• Workflow standardization (v2.0): Standardized workflows for alchemical and geometric routes to enhance reproducibility.
• System scope: Handles protein–ligand interactions and general host–guest complex scenarios.
• Force field compatibility: Supports CHARMM, Amber, OPLS, and GROMOS force fields.
• Simulation engine integration: Generates configurational files compatible with NAMD and Gromacs formats.
• Automation of setup tasks: Automates defining collective variables, preparing input files, monitoring simulations, and post-treatment analyses.
• Post-processing and monitoring: Automated post-treatment processes and generation of intermediate files for convergence monitoring.

Scientific Applications:

• Protein–ligand binding free energy estimation: Quantitative calculation of absolute binding free energies for protein–ligand complexes.
• Host–guest binding studies: Absolute binding free-energy calculations for host–guest systems.
• Computational biology and drug discovery: Reproducible free-energy calculations applicable to computational studies in drug discovery and related fields.

Methodology:

BFEE2 performs molecular dynamics simulations using alchemical transformations and geometric approaches, automates definition of collective variables and input preparation, generates NAMD- and Gromacs-compatible configuration files, produces intermediate files for convergence monitoring, and executes automated post-treatment analyses.