Examples

These notebooks show molforge as it's actually used — multi-step pipelines tying several subpackages together. Each one is self-contained and runnable end-to-end (pre-baked outputs are included so you can read them without re-running).

Notebook	What it shows
Cross-engine validation	Fold the same sequence with ESMFold and AlphaFold, then validate with consensus rules from molforge.validation.
De novo design	RFdiffusion → ProteinMPNN → ESMFold pipeline: scaffold, sequence-design, fold-check, filter.
End-to-end design	Long-form example: from a binding-site spec to a ranked set of designs ready for wet-lab follow-up.

Looking for a guided tour of one subpackage at a time? See the walkthroughs instead — six shorter notebooks, one per subpackage.

The raw notebook files live in notebooks/examples/ on GitHub.