Tutorials¶
Tutorials are the best place to start after reading the installation notes.
If you do not want to install AToM-OpenMM locally, start with the Colab notebooks. They provide guided examples in a browser-based environment and are useful for learning the workflow before setting up a workstation or cluster environment.
Colab Notebooks¶
Local Tutorials¶
The repository tutorials are more detailed and are intended for local or cluster workflows. They are grouped by calculation type below.
ABFE¶
ABFE tutorials estimate the binding free energy of one ligand or molecular partner against a receptor or host. The most up-to-date local ABFE workflow is the FKBP fragments example, which uses the newer YAML setup and variable displacement pattern described in the user guide.
- ABFE FKBP fragments: absolute binding free energies for FKBP ligand fragment complexes using the newer YAML workflow.
- ABFE TEMOA-G1: absolute binding free energy between the TEMOA host and the G1 guest from the SAMPL8 GDCC challenge.
RBFE¶
RBFE tutorials estimate free energy differences between related ligands, guests, peptides, or molecular variants. For current local workflows, start with CDK2 for small-molecule ligand pairs and the TIAM1 protein-peptide example for mutation-like peptide variants.
- RBFE CDK2 inhibitors: relative binding free energies for CDK2 inhibitors using the newer YAML workflow and generated ligand alignment atoms.
- Protein-peptide RBFE TIAM1 variants: relative binding free energies for Syndecan-1-derived peptide variants binding to the TIAM1 PDZ domain.
- RBFE TEMOA G1-G4: relative binding free energy between the G1 and G4 guests to the TEMOA host.
- RBFE ER alpha ligands: relative binding free energies for ligands binding to the ER alpha protein receptor.
Each local tutorial assumes AToM-OpenMM and its runtime dependencies are installed. See Installation before running the repository examples.