free-energy-calculations

You perform ligand binding free energy calculations by executing alchemical simulations for protein-ligand pairs. This Skill computes relative and absolute binding affinities using FEP+ and OpenFE to rank ligand analogs and optimize lead compounds.

Alchemical free energy calculation is a molecular simulation technique that computes the binding affinity of ligands to proteins. It supports FEP+ and OpenFE methods to validate SAR predictions and optimize drug discovery workflows.

Yes, you can use GROMACS and AMBER alongside OpenMM for molecular simulation. The Skill supports these software platforms to execute alchemical free-energy calculations and compare binding affinities for lead optimization.

You rank ligand analogs by running relative binding free energy calculations across the analog series. The Skill uses FEP+ and OpenFE with OpenMM, GROMACS, or AMBER to compute and compare affinities for drug discovery projects.

Yes, the Skill compares alchemical free-energy calculation results with machine learning alternatives like Boltz-2 affinity. This allows you to cross-validate binding affinity predictions and SAR outcomes for lead compound optimization.

Required dependencies include openfe, openmm, gromacs, amber, alchemlyb, pymbar, and rdkit. These libraries provide the molecular simulation engines and analysis tools needed to compute and validate ligand binding free energies.