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    When a domain is not a domain, and why it is important to properly filter proteins in databases: conflicting definitions and fold classification systems for structural domains make filtering of such databases imperative

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    Publication date
    2012-12-01
    Author
    Towse, Clare-Louise
    Daggett, V.
    Keyword
    Computational biology; Dynameome; Intrinsic disorder; Protein structure
    Peer-Reviewed
    Yes
    
    Metadata
    Show full item record
    Abstract
    Membership in a protein domain database does not a domain make; a feature we realized when generating a consensus view of protein fold space with our consensus domain dictionary (CDD). This dictionary was used to select representative structures for characterization of the protein dynameome: the Dynameomics initiative. Through this endeavor we rejected a surprising 40% of the 1,695 folds in the CDD as being non-autonomous folding units. Although some of this was due to the challenges of grouping similar fold topologies, the dissonance between the cataloguing and structural qualification of protein domains remains surprising. Another potential factor is previously overlooked intrinsic disorder; predictions suggest that 40% of proteins have either local or global disorder. One thing is clear, filtering a structural database and ensuring a consistent definition for protein domains is crucial, and caution is prescribed when generalizations of globular domains are drawn from unfiltered protein domain datasets.
    URI
    http://hdl.handle.net/10454/11548
    Version
    No full-text in the repository
    Citation
    Towse C and Daggett V (2012) When a domain is not a domain, and why it is important to properly filter proteins in databases. Bioessays. 34(12):1060-1069.
    Link to publisher’s version
    http://dx.doi.org/10.1002/bies.201200116
    Type
    Article
    Collections
    Life Sciences Publications

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