Citation

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

Primary Citation

GDEE: Gene Discovery and Enzyme Engineering Platform

@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.