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  1. CATH (View Publication)
    Resource Category : Databases -> Structure -> Protein Structure

    Brief Description : Database of automated protein structure classification according to Class (C), Architecture (A), Topology (T) and Homologous superfamily (H).

    Institute/s :
    Biochemistry and Molecular Biology Department, University College London, University of London, Gower Street, London, United Kingdom
    Address of Institute/s :
    Biochemistry and Molecular Biology Department, University College London, University of London, Gower Street, London, UK
    Country : United Kingdom

    Associated Institutes :

    • Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
    • Institute de Fisica de Sao Carlos, Universidade de Sao Paulo, Caixa Postal 369, Sao, Carlos, SP, Brazil
    • European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

    Associated Country : United Kingdom; Brazil


    Authors/Contributors : Alison L. Cuff; Ian Sillitoe; Tony Lewis; Oliver C. Redfern; Richard Garratt; Janet Thornton; Christine A. Orengo
    Contact Email : cuff@biochem.ucl.ac.uk, alisoncuff@yahoo.co.uk
    Year : 2008


  2. CATH
    Resource Category : Databases -> Structure Databases -> Protein structure

    Brief Description : The CATH database of protein domain structures (http://www.biochem.ucl.ac.uk/bsm/cath_new) currently contains 34,287 domain structures classified into 1,383 superfamilies and 3,285 sequence families. Each structural family is expanded with domain sequence relatives recruited from GenBank using a variety of efficient sequence search protocols and reliable thresholds. This extended resource, known as the CATH protein family database (CATH-PFDB) contains a total of 310,000 domain sequences classified into 26,812 sequence families. New sequence search protocols have been designed, based on these intermediate sequence libraries, to allow more regular updating of the classification. Further developments include the adaptation of a recently developed method for rapid structure comparison (GRATH,(1)), based on secondary structure matching, for domain boundary assignment (CATHEDRAL,(2)). The philosophy behind CATHEDRAL is the recognition of recurrent folds already classified in CATH. Benchmarking of CATHEDRAL, using manually validated domain assignments, demonstrated that 43% of domains boundaries could be completely automatically assigned. This is an improvement on a previous consensus approach for which only 10-20% of domains could be reliably processed in a completely automated fashion. Since domain boundary assignment is a significant bottleneck in the classification of new structures, CATHEDRAL will also help to increase the frequency of CATH updates.

    Institute/s :
    Institute of Structural and Molecular Biology, United Kingdom
    Address of Institute/s :
    Institute of Structural and Molecular Biology, United Kingdom
    Country : United Kingdom

    Associated Institutes :

    • Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
    • Institute de Fisica de Sao Carlos, Universidade de Sao Paulo, Caixa Postal 369, Sao, Carlos, SP, Brazil
    • European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

    Associated Country : United Kingdom: Brazil


    Authors/Contributors : Alison L. Cuff; Ian Sillitoe; Tony Lewis; Oliver C. Redfern; Richard Garratt; Janet Thornton; Christine A. Orengo
    Contact Email : cuff@biochem.ucl.ac.uk
    Year : 2008
    Language : English