# Explanation

Explanation pages help you understand why PolyzyMD works the way it does, how
to interpret outputs, and what assumptions or tradeoffs matter.

## Concepts and Design

- [Architecture](../tutorials/architecture.md)
- [Residue Assignment and Chain Conventions](../tutorials/residue_assignment.md)
- [Colored Logging](../tutorials/colored_logging.md)

## Analysis Interpretation and Best Practices

- [Statistical Best Practices for Analysis](../tutorials/analysis_statistics_best_practices.md)
- [RMSF Best Practices](../tutorials/analysis_rmsf_best_practices.md)
- [RMSF Reference Selection](../tutorials/analysis_reference_selection.md)
- [RMSF Verification](../tutorials/analysis_rmsf_verification.md)
- [Catalytic Triad Best Practices](../tutorials/analysis_triad_best_practices.md)

## Experimental Analysis Concepts

These workflows remain available in PolyzyMD, but their interpretation is still
evolving and they should be treated as experimental:

- [Binding Preference](../tutorials/analysis_binding_preference.md)
- [Binding Free Energy](../tutorials/analysis_binding_free_energy.md)
- [Polymer Affinity](../tutorials/analysis_polymer_affinity.md)
- [Exposure Dynamics](../tutorials/analysis_exposure_dynamics.md)

<!-- IMAGE OPPORTUNITY: Add a chain-convention figure (A/B/C/D+), plus a simple
stable-vs-experimental analysis map to orient users before they dive into the
longer conceptual pages. -->

```{toctree}
:hidden:
:maxdepth: 1

Architecture <../tutorials/architecture>
Residue Assignment and Chain Conventions <../tutorials/residue_assignment>
Colored Logging <../tutorials/colored_logging>
Statistical Best Practices for Analysis <../tutorials/analysis_statistics_best_practices>
RMSF Best Practices <../tutorials/analysis_rmsf_best_practices>
RMSF Reference Selection <../tutorials/analysis_reference_selection>
RMSF Verification <../tutorials/analysis_rmsf_verification>
Catalytic Triad Best Practices <../tutorials/analysis_triad_best_practices>
```