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Nucleic Acids Research, 2004, Vol. 32, Database issue D245-D250
© 2004 Oxford University Press

3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes

Keiran Fleming1, Arne Müller1,2, Robert M. MacCallum2 and Michael J. E. Sternberg*,1,2

1 Department of Biological Sciences and Centre for Bioinformatics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK and 2 Biomolecular Modelling Laboratory, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3PX, UK

*To whom correspondence should be addressed at: Biochemistry Building, Department of Biological Sciences, Imperial College London, South Kensington Campus, London SW7 2AY, UK. Tel: +44 20 7594 5212; Fax: +44 20 7594 5264; Email: m.sternberg{at}ic.ac.uk
Present addresses: Arne Müller, Aventis Pharma, Drug Safety Evaluation, 13 quai Jules Guesde, 94403 Vitry-sur-Seine Cedex, France
Robert M. MacCallum, Stockholm Bioinformatics Centre, Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

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.


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