ArticleBMC bioinformatics2007
Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
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- fDETECT webserver: fast predictor of propensity for protein production, purification, and crystallization.BMC bioinformatics · 2018Article
- Unexpected features of the dark proteome.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- A simple recipe for the non-expert bioinformaticist for building experimentally-testable hypotheses for proteins with no known homologs.Journal of structural and functional genomics · 2012Review
- The Proteome Folding Project: proteome-scale prediction of structure and function.Genome research · 2011Article
- Structural characteristics of novel protein folds.PLoS computational biology · 2010Article
- Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling.Journal of computational chemistry · 2010Article
- Identification of recurring protein structure microenvironments and discovery of novel functional sites around CYS residues.BMC structural biology · 2010Article
- Article
- High-throughput crystallography for structural genomics.Current opinion in structural biology · 2009Review
- PSI-2: structural genomics to cover protein domain family space.Structure (London, England : 1993) · 2009Review
- Predicting the energetics of conformational fluctuations in proteins from sequence: a strategy for profiling the proteome.Structure (London, England : 1993) · 2008Article
- The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications.BMC genomics · 2008Article
- The Jpred 3 secondary structure prediction server.Nucleic acids research · 2008Article
- Preservation of protein clefts in comparative models.BMC structural biology · 2008Article
- Gene3D: comprehensive structural and functional annotation of genomes.Nucleic acids research · 2008Article
- Structural genomics and the Protein Data Bank.The Journal of biological chemistryReview
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3 authors.
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Abstract
backgroundStructural genomics initiatives were established with the aim of solving protein structures on a large-scale. For many initiatives, such as the Protein Structure Initiative (PSI), the primary aim of target selection is focussed towards structurally characterising protein families which, so far, lack a structural representative. It is therefore of considerable interest to gain insights into the number and distribution of these families, and what efforts may be required to achieve a comprehensive structural coverage across all protein families.
resultsIn this analysis we have derived a comprehensive domain annotation of the genomes using CATH, Pfam-A and Newfam domain families. We consider what proportions of structurally uncharacterized families are accessible to high-throughput structural genomics pipelines, specifically those targeting families containing multiple prokaryotic orthologues. In measuring the domain coverage of the genomes, we show the benefits of selecting targets from both structurally uncharacterized domain families, whilst in addition, pursuing additional targets from large structurally characterised protein superfamilies.
conclusionThis work suggests that such a combined approach to target selection is essential if structural genomics is to achieve a comprehensive structural coverage of the genomes, leading to greater insights into structure and the mechanisms that underlie protein evolution.
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