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README.md

CATH Tools Build Status Documentation Status

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

Resources
Executable DOWNLOADS
(for 64-bit Linux; chmod them to be executable)
Docs
 
Code
 
secmake
(makes sec files, required by cath-ssap)
Builds
 
Extras repo
 
bioplib
(used to execute the superpositions)

Tools

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, abeit 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

Authors

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:

Feedback

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.