How to Find Active Site Residues of a Protein (4 Methods)

By BioDockify Computational Research Team · September 3, 2026 · Tutorials

Find the active site of any protein for docking: co-crystal ligands, sequence annotations, geometric pocket detection and homolog transfer, then turn the site into a grid box.

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

Key References

• UniProt Consortium. UniProt: the universal protein knowledgebase. Nucleic Acids Res. 2023;51:D523-D531. doi:10.1093/nar/gkac1052
• Berman HM et al. The Protein Data Bank. Nucleic Acids Res. 2000;28:235-242. doi:10.1093/nar/28.1.235
• UniProt knowledgebase and RCSB structure annotations, uniprot.org and rcsb.org.

Scope & Limitations

Automated pocket detection is purely geometric; it cannot distinguish druggable pockets from inert cavities