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Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
Published on: May 6, 2010
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and
Tony E Lewis1, Ian Sillitoe, Antonina Andreeva
1Institute of Structural and Molecular Biology, UCL, 636 Darwin Building, Gower Street, London, WC1E 6BT, UK.
Nucleic Acids Research
|December 4, 2012
Summary
Genome3D integrates UK structural resources for sequence-structure-function analysis. It allows biologists to compare structure prediction methods and maps structural databases, enhancing protein structure research.
Area of Science:
- Bioinformatics
- Structural Biology
- Genomics
Background:
- Protein structure prediction is crucial for understanding biological function.
- Existing resources for structural annotations and 3D models are diverse.
- Integrating these resources offers a unified view of sequence-structure-function relationships.
Purpose of the Study:
- To create a collaborative project (Genome3D) integrating UK-based structural resources.
- To enable comparisons between different protein structure prediction methods.
- To provide the first official mapping between CATH and SCOP structural databases.
Main Methods:
- Integration of leading structure prediction resources (DomSerf, FUGUE, Gene3D, pDomTHREADER, Phyre, SUPERFAMILY).
- Annotation of UniProt sequences with structural domain locations and 3D structures.
- Development of a comparative platform for structure prediction strategies.
- Creation of a mapping between CATH and SCOP superfamilies.
Main Results:
- Genome3D provides structural annotations and 3D models for key model organisms (human, E. coli, yeast).
- The platform facilitates comparison of predictions from multiple resources, highlighting areas of consensus.
- An official mapping between CATH and SCOP identified numerous similar superfamilies (e.g., 532 bronze, 527 silver, 370 gold pairs).
Conclusions:
- Genome3D enhances the reliability of protein structure predictions through comparative analysis.
- The project offers valuable insights into sequence-structure-function relationships.
- The CATH-SCOP mapping provides a crucial resource for structural biologists.
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