Analyse

On-demand

Pairwise structural and sequence comparison of any two PDB chains

What this does

Submit two PDB chain identifiers and StructomeDB will download both structures from RCSB, run Foldseek (structural alignment) and BLASTP (sequence alignment) in both directions, superimpose the structures using the Foldseek rotation matrix, and display the full feature vector with interactive 3D visualisation and 1D alignment tracks.

Results are computed on-demand and are not pre-cached in the database
Expected wait time: 15–60 seconds depending on chain length
Job files are retained for 1 hour then automatically deleted

Enter two PDB chains

Chain A query

Format: PDBID_CHAIN · e.g. 1abc_A

Chain B target

Format: PDBID_CHAIN · e.g. 2xyz_B

⚠ PDB not found

If a PDB ID does not exist or has been superseded, the download will fail and you will see an error on the wait page. Check the ID at rcsb.org.

⚠ Chain not found

The chain ID must match exactly (case-insensitive). Use the RCSB PDB entry page to verify which chains are available for your structure.

⚠ No BLASTP hit

For very divergent proteins, BLASTP may find no significant similarity. The structural alignment (Foldseek) will still be reported and the superposition will be shown.

⚠ Large structures

Chains longer than ~1,000 residues may take up to 2 minutes to process. The wait page will update you with the current step.