Protein structure comparison tools such as SSAP, as used by the Orengo Group in curating CATH.


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Tools


	cath-cluster Map names from previous clusters to new clusters based on (the overlaps between) their members (which may be specified as regions within a parent sequence). Renumber any clusters with no equivalents.
	cath-map-clusters Map names from previous clusters to new clusters based on (the overlaps between) their members (which may be specified as regions within a parent sequence). Renumber any clusters with no equivalents.
	cath-resolve-hits Collapse a list of domain matches to your query sequence(s) down to the non-overlapping subset (ie domain architecture) that maximises the sum of the hits' scores.
	cath-ssap Structurally align a pair of proteins.
	cath-superpose Superpose two or more protein structures using an existing alignment.

Extra Tools

build-test Perform the cath-tools tests (which should all pass, albeit with a few warnings)
cath-assign-domains Use an SVM model on SSAP+PRC data to form a plan for assigning the domains to CATH superfamilies/folds
cath-refine-align Iteratively refine an existing alignment by attempting to optimise SSAP score
cath-score-align Score an existing alignment using structural data

The SSAP algorithm (cath-ssap) was devised by Christine A Orengo and William R Taylor.

Please cite: Protein Structure Alignment, Taylor and Orengo, Journal of Molecular Biology 208, 1-22, PMID: 2769748. (PubMed, Elsevier)

Since then, many people have contributed to this code, most notably:

cath-ssap typically uses DSSP, either by reading DSSP files or via its own implementation of the DSSP algorithms.

Please tell us about your cath-tools bugs/suggestions here.

If you find this software useful, please spread the word and star the GitHub repo.