ArticleBioEssays : news and reviews in molecular, cellular and developmental biology2012
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.
Article in BioEssays : news and reviews in molecular, cellular and developmental biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
5 citing papers in PubMed.
- Protein Fold Usages in Ribosomes: Another Glance to the Past.International journal of molecular sciences · 2024Article
- Conserved patterns and interactions in the unfolding transition state across SH3 domain structural homologues.Protein science : a publication of the Protein Society · 2021Article
- Shared unfolding pathways of unrelated immunoglobulin-like β-sandwich proteins.Protein engineering, design & selection : PEDS · 2019Article
- New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities.Structure (London, England : 1993) · 2016Article
- Protein domain definition should allow for conditional disorder.Protein science : a publication of the Protein Society · 2013Article
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2 authors.
Funding
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.
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