FEPrepare

FEPrepare automates preparation of input files for relative binding free energy (RBFE) calculations to support relative Free Energy Perturbation (FEP) studies for predicting binding-affinity changes in drug discovery.

Key Features:

• Automation: Generates all input files required to run FEP/MD simulations.
• Dual-topology FEP support: Implements the dual-topology scheme for relative Free Energy Perturbation calculations.
• NAMD integration: Produces NAMD-compatible input files and targets the NAMD molecular dynamics engine.
• OPLS‑AA force field: Uses OPLS‑AA force field topology and parameter files for system parameterization.
• Error reduction: Reduces manual setup steps and potential for human error by automating preparatory tasks.

Scientific Applications:

• Drug discovery and lead optimization: Enables RBFE/FEP calculations to predict changes in ligand binding affinity from molecular modifications, supporting design of more potent and selective compounds.

Methodology:

Automated generation of FEP/MD input files using a dual-topology relative FEP scheme with NAMD-compatible outputs and OPLS‑AA topology and parameter files.