Welcome to SWORD2 webserver

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SWift and Optimized Recognition of protein Domains

The SWORD2 partitioning algorithm produces multiple alternative domain assignments for a given protein structure. This unique approach handles ambiguous protein structure partitioning, admitting several solutions. The decomposition of the protein structure into domains is achieved through the hierarchical clustering of Protein Units, evolutionarily preserved structural descriptors at the interface between secondary structures and domains.

See an example of the webserver's output here.

Please use the following reference when citing the SWORD2 webserver:

Cretin, G., Galochkina, T., Vander Meersche, Y., de Brevern, A. G., Postic, G., & Gelly, J. C. (2022).
SWORD2: hierarchical analysis of protein 3D structures. Nucleic acids research, gkac370.
50(W1), W732–W738 10.1093/nar/gkac370

Postic, G., Ghouzam, Y., Chebrek, R., & Gelly, J. C. (2017).
An ambiguity principle for assigning protein structural domains.
Science advances, 3(1), e1600552.10.1126/sciadv.1600552

To launch SWORD on multiple proteins, please use the standalone version freely available on github
Input protein structure (PDB)

Paste example PDB id: 1JX4 (Download PDB file from RCSB database)

Provide either one of the following:

PDB code

AlphaFold Protein Structure Database v4 (UniprotID)

ESM Metagenomic Atlas v2023_02 (MGnifyID)

or upload a PDB/mmCIF file


Default is "A". If the file has no chain, "A" will be used by default.

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