We hope SwissDock has been useful for your research. If so, please cite the following articles:

Bugnon M, Röhrig UF, Goullieux M, Perez MAS, Daina A, Michielin O, Zoete V. SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina. Nucleic Acids Res. 2024 (Web Server issue) , gkae300.

Grosdidier A, Zoete V, Michielin O. SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Res. 2011, 39 (Web Server issue), W270-W277.

If you used Attracting Cavities please cite also:

Röhrig UF, Goullieux M, Bugnon M, Zoete V. Attracting Cavities 2.0: improving the flexibility and robustness for small-molecule docking. J. Chem. Inf. Model., 2023, 63 (12), 3925–3940, DOI: 10.1021/acs.jcim.3c00054

Zoete V, Schuepbach T, Bovigny C, Chaskar P, Daina A, Röhrig UF, Michielin O. Attracting Cavities for Docking. Replacing the Rough Energy Landscape of the Protein by a Smooth Attracting Landscape. J. Comput. Chem., 2016, 37 (4), 437–447. DOI: 10.1002/jcc.24249

If you used Attracting Cavities for covalent docking, please cite also:

Goullieux M, Zoete V, Röhrig UF. Two-Step Covalent Docking with Attracting Cavities. J. Chem. Inf. Model., 2023, 63 (24), 7847-7859. DOI: 10.1021/acs.jcim.3c01055

And the following ones if you used AutoDock Vina:

Eberhardt J, Santos-Martins D, Tillack AF, Forli S. AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. J. Chem. Inf. Model., 2021, 61 (8), 3891–3898, DOI: 10.1021/acs.jcim.1c00203

Trott O, Olson AJ. AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading. J. Comput. Chem., 2010, 31 (2), 455–461, DOI: 10.1002/jcc.21334