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Citations#

If you use DockSuiteX (Python package or GUI application) in your research, please cite it as:

Sinha, M. G. (2025). DockSuiteX: An all-in-one protein-ligand docking package and GUI application [Computer software]. GitHub. https://github.com/MangalamGSinha/DockSuiteX

DockSuiteX builds upon the following excellent tools. Please cite them as appropriate:

AutoDock Vina#

Reference: Trott, O., & 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.

AutoDock4#

Reference: Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of computational chemistry, 30(16), 2785-2791.

P2Rank#

Reference: Krivák, R., & Hoksza, D. (2018). P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure. Journal of cheminformatics, 10(1), 1-12.

Open Babel#

Reference: O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of cheminformatics, 3(1), 1-14.

MGLTools#

Reference: MGLTools. (n.d.). MGLTools software suite. Center for Computational Structural Biology, The Scripps Research Institute. Retrieved November 28, 2025, from https://ccsb.scripps.edu/mgltools/

PDBFixer#

Reference: PDBFixer development team. (n.d.). PDBFixer [software]. https://github.com/openmm/pdbfixer

NGLView#

Reference: Nguyen, H., Case, D. A., & Rose, A. S. (2018). NGLview–interactive molecular graphics for Jupyter notebooks. Bioinformatics, 34(7), 1241-1242.

ProLIF#

Reference: Bouysset, C., & Fiorucci, S. (2021). ProLIF: a library to encode molecular interactions as fingerprints. Journal of Cheminformatics, 13(1), 72.

Data Sources#

RCSB Protein Data Bank#

Reference: Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., ... & Bourne, P. E. (2000). The protein data bank. Nucleic acids research, 28(1), 235-242.

PubChem#

Reference: Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., ... & Bolton, E. E. (2025). PubChem 2025 update. Nucleic acids research, 53(D1), D1516-D1525.

ChEMBL#

Reference: Mendez, D., Gaulton, A., Bento, A. P., Chambers, J., De Veij, M., Félix, E., ... & Leach, A. R. (2019). ChEMBL: towards direct deposition of bioassay data. Nucleic acids research, 47(D1), D930-D940.

How to Cite#

When using DockSuiteX in your research, we recommend citing:

  1. DockSuiteX (main package)
  2. The specific docking engine(s) you used (AutoDock Vina and/or AutoDock4)
  3. P2Rank if you used pocket prediction
  4. ProLIF if you used interaction profiling
  5. Other tools as appropriate for your workflow