3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes.
The 3D-GENOMICS database (http://www.sbg.bio. ic.ac.uk/3dgenomics/) provides structural annotations for proteins from sequenced genomes. In August 2003 the database included data for 93 proteomes. The annotations stored in the database include homologous sequences from various sequence databases, domains from SCOP and Pfam, patterns from Prosite and other predicted sequence features such as transmembrane regions and coiled coils. In addition to annotations at the sequence level, several precomputed cross- proteome comparative analyses are available based on SCOP domain superfamily composition. Annotations are available to the user via a web interface to the database. Multiple points of entry are available so that a user is able to: (i) directly access annotations for a single protein sequence via keywords or accession codes, (ii) examine a sequence of interest chosen from a summary of annotations for a particular proteome, or (iii) access precomputed frequency-based cross-proteome comparative analyses.
Fleming
Keiran
K
Department of Biological Sciences and Centre for Bioinformatics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
Müller
Arne
A
MacCallum
Robert M
RM
Sternberg
Michael J E
MJ
D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology; D030562:Databases, Protein; D016678:Genome; D023281:Genomics; D006801:Humans; D016247:Information Storage and Retrieval; D020407:Internet; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D020543:Proteome; D040901:Proteomics; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D014584:User-Computer Interface
D011506:Proteins; D020543:Proteome