ProteinStructure/about.md

# ProteinStructure — Test Entries

Species-independent 3D protein structures, organized by PDB ID. Each entry
directory contains the same structure in two formats:

- `<PDB_ID>.pdb` — legacy PDB format (fixed-column text)
- `<PDB_ID>.cif` — mmCIF format (preferred for modern tooling and large complexes)

Both files describe the same atomic coordinates; choose by tool compatibility.

## Available Entries

| PDB ID | Source Organism | Molecule | Method | Notes |
|--------|-----------------|----------|--------|-------|
| `1AKI` | *Gallus gallus* (chicken) | Hen egg-white lysozyme | X-ray diffraction, 1.5 Å | Classic small enzyme; widely used in MD tutorials (e.g., GROMACS lysozyme tutorial). |
| `1CRN` | *Crambe hispanica* subsp. *abyssinica* | Crambin | X-ray diffraction | Very small (46 residues); fast to parse, good smoke-test entry. |

## Suggested Uses

- Structure parsing (`Bio.PDB`, `gemmi`, `MDAnalysis`)
- Format conversion (PDB ↔ mmCIF)
- Visualization (PyMOL, ChimeraX, NGLview)
- Secondary-structure assignment (DSSP), surface/pocket analysis
- Lightweight inputs for molecular dynamics setup demos

## Notes

These entries are **not** linked to the reference genomes under
`SaccharomycesCerevisiae/` or `StaphylococcusAureus/`. They are keyed by PDB
ID, not by species.

Source: RCSB PDB (https://www.rcsb.org/).