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3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes
Keiran Fleming1, Arne Müller, Robert M MacCallum
1Department of Biological Sciences and Centre for Bioinformatics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
Nucleic Acids Research
|December 19, 2003
Summary
The 3D-GENOMICS database offers structural protein annotations for 93 proteomes, aiding in comparative genomics. It provides sequence features and cross-proteome analyses via a user-friendly web interface.
Area of Science:
- Bioinformatics
- Structural Biology
- Genomics
Background:
- Protein structural annotation is crucial for understanding genomic data.
- Databases integrating sequence and structural features facilitate comparative analysis.
- The 3D-GENOMICS database consolidates diverse protein information.
Purpose of the Study:
- To present the 3D-GENOMICS database, a resource for structural protein annotations.
- To detail the types of annotations and comparative analyses available.
- To describe the database's web interface and access points.
Main Methods:
- Data compilation from sequenced genomes and various sequence databases.
- Inclusion of domain information from SCOP and Pfam.
- Prediction of sequence features like transmembrane regions and coiled coils.
Main Results:
- The database contains structural annotations for proteins across 93 proteomes (as of August 2003).
- Annotations include homologous sequences, SCOP/Pfam domains, Prosite patterns, and predicted features.
- Precomputed cross-proteome comparative analyses based on SCOP domain superfamily composition are available.
Conclusions:
- The 3D-GENOMICS database serves as a valuable resource for exploring protein structures and functions within and across proteomes.
- Its comprehensive annotations and comparative analyses support genomic research.
- The web interface allows flexible access to detailed protein and proteome information.