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cath-tools

Protein structure comparison tools such as SSAP and SNAP

https://github.com/uclorengogroup/cath-tools

Science Score: 28.0%

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    Low similarity (9.1%) to scientific vocabulary

Keywords

alignment bioinformatics biology cath cath-resolve-hits orengo pdb protein ssap structure superposition ucl
Last synced: 6 months ago · JSON representation ·

Repository

Protein structure comparison tools such as SSAP and SNAP

Basic Info
Statistics
  • Stars: 51
  • Watchers: 10
  • Forks: 14
  • Open Issues: 21
  • Releases: 33
Topics
alignment bioinformatics biology cath cath-resolve-hits orengo pdb protein ssap structure superposition ucl
Created over 10 years ago · Last pushed over 2 years ago
Metadata Files
Readme Changelog License Citation

README.md

CATH Tools Build Status Documentation Status

Overview

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

| | | | | |:-- |:-- |:-- |:-- | | Executable DOWNLOADS
(for Linux/Mac; chmod them to be executable) | Docs
  | Code
  | Extras repo
  |

Tools

| | | |:-- |:-- | |

| cath-cluster
Complete-linkage cluster arbitrary data. | |
| 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

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:

Acknowledgements

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

cath-cluster uses Fionn Murtagh's reciprocal-nearest-neighbour algorithm (see Multidimensional clustering algorithms, volume 4 of Compstat Lectures. Physica-Verlag, Würzburg/ Wien, 1985. ISBN 3-7051-0008-4) as described and refined in Daniel Müllner's Modern hierarchical, agglomerative clustering algorithms (2011, arXiv:1109.2378).

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.

Owner

  • Name: UCLOrengoGroup
  • Login: UCLOrengoGroup
  • Kind: organization

Citation (CITATION.md) 

Citation
--------

If you use `cath-tools`, please star the GitHub repo and cite it in any related publications.

If you use `cath-ssap` in your work, please cite the following in any related publications:

    "Protein Structure Alignment", Taylor and Orengo [1989]
    Journal of Molecular Biology 208, 1-22
    PMID: 2769748

Acknowledgements
----------------

Algorithm devised by Christine A Orengo and William R Taylor

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)

`cath-cluster` uses Fionn Murtagh's reciprocal-nearest-neighbour algorithm (see [Multidimensional clustering algorithms, volume 4 of Compstat Lectures.
Physica-Verlag, Würzburg/ Wien, 1985. ISBN 3-7051-0008-4](http://www.multiresolutions.com/strule/MClA/)) as described and refined in Daniel Müllner's [Modern hierarchical, agglomerative clustering algorithms](https://arxiv.org/abs/1109.2378) (2011, arXiv:1109.2378).

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