gmx_MMPBSA

gmx_MMPBSA performs end-state binding free energy calculations and decomposition to estimate binding affinities and thermodynamic contributions from GROMACS trajectories.

Key Features:

• Versatile Solvation Models: Supports Poisson-Boltzmann (PB), Generalized Born (GB), and 3D-RISM solvation models.
• Comprehensive Free Energy Calculations: Performs binding free energy calculations, stability assessments, and computational alanine scanning for protein-ligand complexes.
• Entropy Corrections and Decomposition: Implements entropy corrections and binding free energy decomposition to provide per-residue and component thermodynamic profiles.
• Advanced Analysis Methods: Includes alanine scanning with variable dielectric constants and interaction entropy calculations to refine relative binding free energy estimates.
• Integrated Analysis Utilities: Provides gmx_MMPBSA_test for example calculations and test cases and gmx_MMPBSA_ana for generating graphical representations of output data.

Scientific Applications:

• Drug Discovery: Estimates binding affinities and decomposed thermodynamic contributions to support ligand prioritization and rational drug design.
• Structural Biology: Analyzes molecular interactions and stability of biomolecular complexes at atomic resolution using GROMACS trajectories.
• Mutational Analysis: Uses computational alanine scanning and decomposition to identify key residues and predict effects of mutations on protein-ligand binding.

Methodology:

Applies molecular mechanics Poisson-Boltzmann and Generalized Born surface area (MM/PB(GB)/SA) calculations to GROMACS trajectories, with options for entropy corrections, binding free energy decomposition, computational alanine scanning, 3D-RISM, and interaction entropy calculations.