Tutorials

Below is a collection of tutorials that demonstrate key elements of OpenFE tooling.

You can clone the Example Notebooks Repository to explore any of these tutorials interactively.

Relative Free Energies

• Python API Showcase: Start here! An introduction to OpenFE’s Python API and approach to performing a relative binding free energy calculation.

• RBFE with the Python API: A step-by-step tutorial for using the Python API to calculate relative binding free energies for TYK2.

• RBFE with the CLI: A step-by-step tutorial for using the OpenFE command line interface (CLI) to calculate relative binding free energies for TYK2.

Absolute Free Energies

• Absolute Solvation Free Energy Protocol: A walk-through of calculating the hydration free energy of a benzene ligand.

Molecular Dynamics (MD)

• MD protocol: A walk-through of running a conventional (non-alchemical) MD simulation of benzene bound to T4-lysozyme L99A.

Post-Simulation Analysis

• Cinnabar tutorial: A tutorial for using the cinnabar Python package to analyze (e.g. generating MLE estimates of absolute free energies) and plot networks of relative free energy results.

Generating Partial Charges

• Generating Partial Charges CLI tutorial: how to use the CLI to assign and store partial charges for mall molecules which can be used throughout the OpenFE ecosystem.