Examples

Curated examples and Git LFS

The repository includes examples for protein-ligand, cofactor-aware, biological assembly, and PROTAC workflows. Large example assets may require Git LFS.

Curated examples

Example	System and lesson
Example 1	CPD32_9G94 with A1D; standard protein-ligand setup through analysis and figurebook.
Example 2	9UWJ / AVPR1A with A1E and CLR; retained cofactor/context workflow.
Example 3	1URN; RNA/protein biological assembly workflow.
Example 4	5T35 with PTC; PROTAC ternary-complex workflow.

Git LFS check

Copy command

git lfs version
git lfs install
git lfs pull

Reproduce the figurebook demo

Start with Example 1, use a short production run, run 3A analysis, run NETWORX when contact tables exist, and finish with 4PDF4MD.py. Then compare your outputs with the packaged completed_run folder.

Website walkthrough

The examples page provides copyable commands for each curated example.

Open examples