# FastMDXplora documentation

> **F**ully **A**utomated **Sy**s**T**em for **M**olecular **D**ynamics e**Xplora**tion

FastMDXplora explores a protein's behavior end to end from a single command.
Given a structure (or just a PDB ID) it performs molecular dynamics
exploration all the way through setup, simulation, analysis, and reporting,
then hands back publication-ready results.

```{toctree}
:maxdepth: 2
:caption: Getting started

installation
phases
usage_examples
configuration
```

```{toctree}
:maxdepth: 2
:caption: Reference

api
```

## Quick links

- [GitHub repository](https://github.com/aai-research-lab/FastMDXplora)
- [PyPI: fastmdxplora](https://pypi.org/project/fastmdxplora/)
- [PyPI: fastmdx (alias)](https://pypi.org/project/fastmdx/)
- [Foundational paper (JCC 2026)](https://doi.org/10.1002/jcc.70350)

## Citation

If you use FastMDXplora in your work, please cite:

> Aina, A.; Kwan, D. *FastMDAnalysis: Software for Automated Analysis of Molecular Dynamics Trajectories.* J. Comput. Chem. **2026**, 47, e70350. DOI: [10.1002/jcc.70350](https://doi.org/10.1002/jcc.70350)