Molecular Dynamics Affinity Package Documentation

The Molecular Dynamics Affinity Floes package brings physics-based molecular dynamics (MD) simulation and binding affinity predictions into Orion. It provides ready-to-run Floes for preparing protein-ligand systems, sampling their behavior with MD, and turning those simulations into actionable predictions for ligand prioritization.

At the center of the package is free-energy nonequilibrium switching (FE-NES), which combines equilibrium end-state simulations, alchemical edge mapping, and nonequilibrium switching to provide relative binding free energy predictions in a single run. The components can also be used in stages: run MD first, inspect or extend the resulting trajectories, make interactive edge maps, recover interrupted calculations, and regenerate affinity reports without repeating completed work.

This package also includes trajectory analysis and induced-fit docking workflows for understanding ligand stability, protein-ligand interactions, and binding-site adaptation. Together, these tools let you move from prepared structures to simulation results, comparative affinity estimates, and interpretable reports within the Orion environment.

For more information on getting started and using the package, see the tutorials and the floe documentation below.