CSA (Comparative Structural Alignment) is a webserver for computing and comparing protein structure alignments. CSA is able to compute score-optimal alignments with respect to various inter-residue distance-based scoring schemes. Currently supported scoring schemes are;
  • Contact map overlap (CMO)
  • DALI elastic similarity scoring
  • MATRAS scoring
  • PAUL scoring

A large number of alignment statistics and properties are computed in order to facilitate their comparison. Additional alignments can be uploaded and integrated in the comparison.
If you want to compute your alignments locally, the stand-alone alignment programs can be downloaded here. Online evaluation is currently not available, please use the stand-alone programs.

If you find CSA useful for your work, please cite
I. Wohlers, N. Malod-Dognin, R. Andonov and G.W. Klau. CSA: comprehensive comparison of pairwise protein structure alignments. Nucleic Acids Res, 40(Web Server issue):303-309, 2012.


The input consists of two entries from the protein data bank PDB. Specify each entry by either giving a PDB identifier or by uploading a PDB file.

Either use the PDB identifer...
(e.g. 1byo)
(e.g. 1pla)

... or upload a PDB file
PDB file 1 PDB file 2

Specify the chains
Chain 1
(e.g. A)
Chain 2
(e.g. A)

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