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CATHEDRAL specifications

Information


Unique identifier OMICS_13712
Name CATHEDRAL
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Oliver Redfern <>

Publication for CATHEDRAL

CATHEDRAL citations

 (6)
library_books

The history of the CATH structural classification of protein domains

2015
PMCID: 4678953
PMID: 26253692
DOI: 10.1016/j.biochi.2015.08.004

[…] pdb, by employing a filter that only allows comparison of proteins having sufficiently similar secondary structure arrangements and connectivity in their common structural core . this new approach – cathedral – is nearly 1000 times faster than ssap allowing cath to remain up to date with the pdb., the scop classification was largely constructed using manual evaluation of domain relationships […]

library_books

1,000 structures and more from the MCSG

2011
PMCID: 3024214
PMID: 21219649
DOI: 10.1186/1472-6807-11-2

[…] novel and belongs to a new structural sub-group (ssg). both mcsg domains assigned to cath and unassigned mcsg pdb chains are compared to a representative library of cath domains (s35 reps) using cathedral [] as a fast filter for significant structural similarity. the best matches by cathedral are then structurally aligned and superposed using the more computationally expensive and accurate […]

library_books

The CATH Hierarchy Revisited—Structural Divergence in Domain Superfamilies and the Continuity of Fold Space

2009
PMCID: 2741583
PMID: 19679085
DOI: 10.1016/j.str.2009.06.015

[…] necessary for the more challenging structures., probably the best known method for measuring structural similarity is the root mean square deviation (rmsd) (). structures are first aligned using the cathedral structure comparison algorithm (), and the alignment is used to guide a superposition of the domains using the mclachlan algorithm () in order to calculate rmsd. since rmsd […]

library_books

Protein function annotation by homology based inference

2009
PMCID: 2688287
PMID: 19226439
DOI: 10.1186/gb-2009-10-2-207

[…] resources use some automated protocols, domain assignments are primarily made by expert manual validation. cath differs from scop only in its use of structure-comparison algorithms (for example, cathedral []) and of hidden markov model-based approaches to provide guidance to curators during classification (see box ). creating functional subfamilies within superfamilies in cath or scop […]

library_books

The CATH classification revisited—architectures reviewed and new ways to characterize structural divergence in superfamilies

2008
PMCID: 2686597
PMID: 18996897
DOI: 10.1093/nar/gkn877

[…] the last 10 years and the percentage of non-redundant structures deposited adopting a novel fold. table 2., we have further improved our domain boundary prediction and fold assignment algorithm, cathedral (), which is used to guide curators in the manual classification process. whole pdb structures are scanned against a library of representatives from the cath database to recognize […]

library_books

The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function

2008
PMCID: 2518264
PMID: 18974821
DOI: 10.1371/journal.pcbi.1000160

[…] structural comparisons, using the protein data bank or structure classification databases (scop , cath ) as a source. among the most used structural alignment methods are ssm , fatcat , dali , and cathedral (see for a comparison of the performance of several methods). in general, it is suggested to use more than one method since different methods may capture different valid matches. […]


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CATHEDRAL institution(s)
Department of Biochemistry and Molecular Biology, University College London, London, UK; Department of Mathematical Sciences and Biological Sciences, University of Essex, Wivenhoe Park, Colchester, UK
CATHEDRAL funding source(s)
This work was partly funded by an Engineering and Physical Sciences Research Council (EPSRC) studentship, a Biotechnology and Biological Sciences Research Council (BBSRC) studentship and the Medical Research Council.

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