Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint

<p>Abstract</p> <p>Background</p> <p>Structural 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 towar...

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Main Authors: Orengo Christine A, Lewis Tony A, Marsden Russell L
Format: Article
Language:English
Published: BMC 2007-03-01
Series:BMC Bioinformatics
Online Access:http://www.biomedcentral.com/1471-2105/8/86
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spelling doaj-553179f21ab34f35a7e32cf7f79c20c52020-11-24T21:19:08ZengBMCBMC Bioinformatics1471-21052007-03-01818610.1186/1471-2105-8-86Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpointOrengo Christine ALewis Tony AMarsden Russell L<p>Abstract</p> <p>Background</p> <p>Structural 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.</p> <p>Results</p> <p>In 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 uncharacterised 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 uncharacterised domain families, whilst in addition, pursuing additional targets from large structurally characterised protein superfamilies.</p> <p>Conclusion</p> <p>This 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.</p> http://www.biomedcentral.com/1471-2105/8/86
collection DOAJ
language English
format Article
sources DOAJ
author Orengo Christine A
Lewis Tony A
Marsden Russell L
spellingShingle Orengo Christine A
Lewis Tony A
Marsden Russell L
Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint
BMC Bioinformatics
author_facet Orengo Christine A
Lewis Tony A
Marsden Russell L
author_sort Orengo Christine A
title Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint
title_short Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint
title_full Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint
title_fullStr Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint
title_full_unstemmed Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint
title_sort towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint
publisher BMC
series BMC Bioinformatics
issn 1471-2105
publishDate 2007-03-01
description <p>Abstract</p> <p>Background</p> <p>Structural 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.</p> <p>Results</p> <p>In 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 uncharacterised 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 uncharacterised domain families, whilst in addition, pursuing additional targets from large structurally characterised protein superfamilies.</p> <p>Conclusion</p> <p>This 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.</p>
url http://www.biomedcentral.com/1471-2105/8/86
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