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Product specification

The CATHEDRAL program generates a structural alignment of two protein structures in standard Protein Data Bank (PDB) format. The output shows the structural similarity (as a native vector score and RMSD), as well as the sequence identity and the total number of aligned amino acids. The alignment shows equivalent amino acids and their corresponding secondary structures (identical residues).

Product description

CATHEDRAL uses structure comparison (rather than sequence comparison) to align proteins of known structure in order to correctly align their sequences. This is of particular use when two proteins, whose structures have been determined by either X-ray crystallography or NMR spectroscopy, have similar structures but dissimilar sequences.

CATHEDRAL is used to generate alignments for the popular CATH structure classification. The program is based on the double-dynamic alignment approach using the SSAP algorithm. It  has been shown to be at least as sensitive at detecting homologues (proteins related through evolution) as current best-in-class structure alignment algorithms. Furthermore, it was shown to outperform these algorithms in benchmark testing against manually curated alignments from the BaliBase database. The program is useful for pharmaceutical and biotech companies looking to explore drug interations and de novo protein design.

More details can be found in the README.pdf file available further down this page.

A public version of the CATHEDRAL webserver is accessible at

Product requirements

  • 32/64 bit Linux operating system (running at least v2.6.9 kernel). e.g. Redhat Enterprise 4.7
  • Perl v5.8.x
  • C shell

Windows and Mac versions are available on request although there may be some system limitations. Please use the "Contact Product Support" button on this page to request further information, including in your message the specifics of your operating system.

If installation support is required, this can be organised with the program author through our partner organisation UCL Consultants Ltd. For information on rates and availability, please contact them on 020 7679 9794 or, quoting "XIP product CATHEDRAL"





Protein Structure Comparison Software

Please check carefully that the terms you select correspond to your intended use of the product.

UCLB Licence CMR-A 1.02

For internal commercial research use. Does not allow use on behalf of a third party. Quoted licence fee covers a single machine installation with 1 named user. For additional users and/or additional machines, please select the P.O.A. licence option below.

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Further details
Term: 12 months
Seats: 1 seat(s)

Price excl. VAT: £2400.00

UCLB Licence CMR-A 1.02

For internal commercial research use. Does not allow use on behalf of a third party.

View Terms

Further details
Term: 12 months
Seats: 1+ seats

Price excl. VAT: P.O.A. (price on application)

Please contact us before adding this licence to your basket.