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Published on: August 15, 2019
Gene3D: comprehensive structural and functional annotation of genomes
Corin Yeats1, Jonathan Lees, Adam Reid
1UCL, Department of Molecular Biology & Biochemistry, Darwin Building, Gower St, London, UK. yeats@biochem.ucl.ac.uk
Nucleic Acids Research
|November 23, 2007
Summary
Gene3D offers extensive protein sequence annotation, integrating structural data from CATH and functional information from multiple resources. This comprehensive resource aids in exploring protein relationships and functions across diverse genomes.
Area of Science:
- * Bioinformatics and Structural Genomics
- * Computational Biology and Protein Annotation
Background:
- * Protein sequence annotation is crucial for understanding biological function and evolution.
- * Existing databases often lack comprehensive integration of structural and functional data.
- * The CATH (Class, Architecture, Topology, Homologous superfamily) database provides a hierarchical classification of protein domains.
Purpose of the Study:
- * To present Gene3D, a resource for comprehensive structural and functional annotation of protein sequences.
- * To integrate diverse data sources for enhanced protein investigation.
- * To provide a user-friendly website for flexible data exploration.
Main Methods:
- * Structural annotation by scanning protein sequences against the CATH domain profile-Hidden Markov Model (HMM) library.
- * Integration of supplementary data including Pfam-A, non-domain structural predictions, and experimental data from UniProt.
- * Incorporation of various protein annotation resources: protein-protein interactions, Gene Ontology (GO) functional assignments, KEGG pathways, FUNCAT, and microarray expression data.
Main Results:
- * Gene3D provides integrated structural and functional annotation for millions of proteins across 527 genomes.
- * The CATH database enables inference of ancient and divergent homology relationships.
- * The re-designed website offers flexible and clear data access, with genome-specific or cross-database search capabilities.
Conclusions:
- * Gene3D serves as a valuable, integrated resource for comprehensive protein analysis.
- * The platform facilitates deeper investigations into protein structure-function relationships and evolutionary connections.
- * Enhanced data accessibility through the new website supports broader biological research.
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