CaFE

CaFE calculates binding free energies using end-point free energy methods MM/PBSA and LIE to predict ligand–protein binding affinities for structure-based drug design.

Key Features:

• End-point free energy methods: Implements MM/PBSA (Molecular Mechanics/Poisson-Boltzmann Surface Area) and LIE (Linear Interaction Energy) for binding free energy calculations.
• Integration with VMD and NAMD: Operates as a VMD plugin and integrates with NAMD-generated molecular dynamics trajectories.
• Support for multiple file formats: Handles static coordinate files and molecular dynamics trajectory formats produced by various simulation packages.
• Force field parameter support: Accepts diverse force field parameters for molecular mechanics energy evaluations.
• Implementation language: Implemented in Tcl.

Scientific Applications:

• Structure-based drug design: Predicts ligand–protein binding affinities to support identification and optimization of drug candidates.
• Ligand–protein binding affinity evaluation: Evaluates binding affinities of ligands to target proteins using MM/PBSA and LIE.
• Molecular dynamics analysis: Analyzes energetics of ligand–protein complexes derived from molecular dynamics trajectories.

Methodology:

Implements end-point binding free energy calculations using MM/PBSA (Molecular Mechanics/Poisson-Boltzmann Surface Area) and LIE (Linear Interaction Energy) applied to static coordinate files and molecular dynamics trajectories.