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Open Access Research article

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

Russell L Marsden*, Tony A Lewis and Christine A Orengo

Author Affiliations

Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK

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BMC Bioinformatics 2007, 8:86  doi:10.1186/1471-2105-8-86

Published: 9 March 2007

Abstract

Background

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.

Results

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.

Conclusion

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.