(for 64-bit Linux; chmod them to be executable)
(makes sec files, required by cath-ssap)
(used to execute the superpositions)
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.
Structurally align a pair of proteins.
Superpose two or more protein structures using an existing alignment.
build-testPerform the cath-tools tests (which should all pass, albeit with a few warnings)
cath-assign-domainsUse an SVM model on SSAP+PRC data to form a plan for assigning the domains to CATH superfamilies/folds
cath-refine-alignIteratively refine an existing alignment by attempting to optimise SSAP score
cath-score-alignScore an existing alignment using structural data
The SSAP algorithm (
cath-ssap) was devised by Christine A Orengo and William R Taylor.
Since then, many people have contributed to this code, most notably:
- Tony E Lewis (2011 - ....)
- Oliver C Redfern (~2003 - 2011)
- James E Bray, Ian Sillitoe (~2000 - 2003)
- Andrew C R Martin (considerable edits around 2001)
Superpositions are currently performed using the bioplib library.
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.