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Related Experiment Video

Updated: Dec 16, 2025

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

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Published on: August 15, 2019

The Genome3D Consortium for Structural Annotations of Selected Model Organisms.

Vaishali P Waman¹, Tom L Blundell², Daniel W A Buchan³

¹Institute of Structural and Molecular Biology, University College London, London, UK.

Methods in Molecular Biology (Clifton, N.J.)

|July 5, 2020

Summary

The Genome3D consortium offers a unified portal for protein structure prediction and annotation across ten model organisms. This resource integrates multiple bioinformatics tools, aiding researchers in comparative analysis and understanding protein structure-function relationships.

Keywords:

Annotation CATH Fold recognition Function prediction Hidden Markov model Homology modeling Protein domain Protein family Protein structure prediction Protein superfamily SCOP Superfamily mapping

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Area of Science:

Structural Bioinformatics
Computational Biology
Genomics

Background:

Protein structure prediction and annotation are crucial for understanding biological function.
Existing resources are often fragmented, hindering comprehensive analysis.
The Genome3D consortium addresses this by integrating multiple prediction and annotation tools.

Purpose of the Study:

To create a common portal for accessing predicted protein models and annotations.
To compare structural classifications between CATH and SCOP databases.
To provide a consensus mapping of protein superfamilies.

Main Methods:

Integration of multiple protein structure prediction and annotation resources (CATH-Gene3D, DOMSERF, pDomTHREADER, PHYRE, SUPERFAMILY, FUGUE/TOCATTA, VIVACE).
Utilizing SCOP- and CATH-based protein domain assignments.
Comparative analysis of structural classifications from CATH and SCOP databases.

Main Results:

Development of a unified portal, Genome3D, for protein structure prediction and annotation.
Identification of 1429 consensus superfamilies through CATH/SCOP mapping.
Provision of structural annotations for ten model organisms, including Homo sapiens and E. coli.

Conclusions:

Genome3D serves as a valuable gateway for comparative assessment of protein structure predictions.
The resource facilitates broader perspectives on protein structure-function relationships in model organisms.
This collaborative effort enhances the accessibility and utility of protein structure data.