SwissDock Tutorial: Free Protein-Ligand Docking Web Server

By BioDockify Computational Research Team · September 19, 2026 · Tutorial

SwissDock tutorial: submit a docking job on the free SwissDock web server, prepare inputs correctly, read EAD and full fitness scores, and export poses for visualization.

Read the complete article with tables, code and references on BioDockify.

Key References

• Grosdidier, A. et al. SwissDock, a protein-small molecule docking web service. Nucleic Acids Res. 39, W270–W277 (2011). DOI: 10.1093/nar/gkr366
• Zoete, V. et al. SwissDock with the CHARMM force field. J. Comput. Chem. 32, 2119–2128 (2011). DOI: 10.1002/jcc.21816
• Grosdidier, A. & Michielin, O. EADock: docking with a multi-objective evolutionary algorithm. Proteins 67, 1260–1269 (2007). DOI: 10.1002/prot.21361

Scope & Limitations

No user control over the search box — binding modes are global or cavity-restricted, not custom boxes Queue times vary from minutes to hours; batch work is impractical on the public server