Citation
========

If you use GDEE in your research, please cite the following:

Primary Citation
----------------

**GDEE: Gene Discovery and Enzyme Engineering Platform**

.. code-block:: bibtex

    @article{souza2025gdee,
      title={GDEE: A Structure-Based Platform for Gene Discovery and Enzyme Engineering},
      author={Souza, Caio S and Correia, Jo{\~a}o PG and Rocha, Isabel and Lousa, Diana and Soares, Cl{\'a}udio M},
      journal={bioRxiv},
      pages={2025--09},
      year={2025},
      publisher={Cold Spring Harbor Laboratory}
    }

**Text Citation:**

Souza, C. S. (2025). GDEE: A Structure-Based Platform for Gene Discovery and Enzyme Engineering. *bioRxiv*. https://doi.org/10.1101/2025.09.09.675117 

Project Acknowledgment
----------------------

This platform was developed under the **ShikiFactory 100** project, funded by the European Union's Horizon 2020 research and innovation programme under grant agreement number **814408**.


References
----------

GDEE relies on several key computational tools and libraries. If you use GDEE extensively, please consider citing the following dependencies:

**MODELLER**
   Webb, B. and Sali, A. (2016). Comparative Protein Structure Modeling Using MODELLER. *Current Protocols in Bioinformatics*, 54, 5.6.1-5.6.37. doi: 10.1002/cpbi.3

**AutoDock Vina**
   Trott, O. and Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. *Journal of Computational Chemistry*, 31(2), 455-461. doi: 10.1002/jcc.21334

**MDAnalysis**
   Michaud-Agrawal, N., Denning, E. J., Woolf, T. B. and Beckstein, O. (2011). MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. *Journal of Computational Chemistry*, 32, 2319-2327. doi: 10.1002/jcc.21787

**VoroMQA** 
   Olechnovič, K. and Venclovas, Č. (2017). VoroMQA: Assessment of protein structure quality using interatomic contact areas. *Proteins: Structure, Function, and Bioinformatics*, 85(6), 1131-1145. doi: 10.1002/prot.25278

**NumPy**
   Harris, C. R., Millman, K. J., van der Walt, S. J., et al. (2020). Array programming with NumPy. *Nature*, 585, 357-362. doi: 10.1038/s41586-020-2649-2

**BioPython**
   Cock, P. J. A., Antao, T., Chang, J. T., et al. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. *Bioinformatics*, 25(11), 1422-1423. doi: 10.1093/bioinformatics/btp163

**Open Drug Discovery Toolkit (ODDT)**
   Wójcikowski M, Zielenkiewicz P, Siedlecki P. Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field. J Cheminform. 2015 Jun 22;7:26. doi: 10.1186/s13321-015-0078-2. PMID: 26101548; PMCID: PMC4475766.