Tutorials

OpenFE has several tutorial notebooks which are maintained on our Example Notebooks repository.

Here is a list of key tutorials which cover the different aspects of the OpenFE tooling:

Relative Free Energies

Python API Showcase

Our shocase notebook walks users through how to use the main Python API components of OpenFE to create a relative binding free energy calculation.

Relative Free Energies CLI tutorial

The Relative Free Energies with the OpenFE CLI tutorial walks users through how to use the OpenFE command line to calculate relative binding free energies of various ligands against the TYK2 target.

Associated with it is also a notebook for how to achieve the same outcomes using the Python API.

Absolute Free Energies

Absolute Solvation Free Energies

The Absolute Solvation Free Energy Protocol tutorial walks users through how to calculate the hydration free energy of a benzene ligand.

Molecular Dynamics (MD)

The MD protocol tutorial walks users through how to run a conventional (non-alchemical) MD simulation of benzene bound to T4-lysozyme L99A in OpenFE.

Post Simulation Analysis

Analyzing and Plotting RFE Networks with Cinnabar

The Cinnabar tutorial demonstrates how to use the Cinnabar Python package to analyze (e.g. generating MLE estimates of absolute free energies) and plot networks of relative free energy results.