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Related Experiment Video

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Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

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Published on: May 6, 2010

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

Russell L Marsden¹, Tony A Lewis, Christine A Orengo

¹Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK. marsden@biochem.ucl.ac.uk

BMC Bioinformatics

|March 14, 2007

Summary

Structural genomics aims to solve protein structures. A combined approach targeting uncharacterized and large protein families is essential for comprehensive structural coverage and evolutionary insights.

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Area of Science:

Structural biology
Genomics
Protein science

Background:

Structural genomics initiatives aim for large-scale protein structure determination.
The Protein Structure Initiative (PSI) focuses on structurally uncharacterized protein families.
Understanding the distribution of these families is crucial for comprehensive structural coverage.

Purpose of the Study:

To assess the number and distribution of protein families lacking structural representation.
To determine the accessibility of uncharacterized families to high-throughput structural genomics pipelines.
To evaluate strategies for achieving comprehensive structural coverage of protein families.

Main Methods:

Comprehensive domain annotation of genomes using CATH, Pfam-A, and Newfam domain families.
Analysis of structurally uncharacterized families accessible to high-throughput pipelines.
Measurement of domain coverage across genomes.

Main Results:

Derived comprehensive domain annotation of genomes.
Identified proportions of uncharacterized families accessible to high-throughput pipelines, particularly those with prokaryotic orthologues.
Demonstrated benefits of selecting targets from both uncharacterized and large characterized protein superfamilies for domain coverage.

Conclusions:

A combined target selection strategy is essential for structural genomics.
This approach is key to achieving comprehensive structural coverage of genomes.
Leads to greater insights into protein structure and evolutionary mechanisms.