3D-GENOMICS is a database containing structural annotations for the proteomes of just under 100 organisms. Using data derived from public databases of translated genomic sequences, representatives from the major branches of Life are included: Prokaryota, Eukaryota and Archaea.

The annotations stored in the database may be accessed in a number of ways. The help page provides information on how to access the database.

3D-GENOMICS is now part of a larger project, called e-Protein . The project brings together similar databases at three sites: Imperial College London , University College London and the European Bioinformatics Institute . e-Protein's mission statement is "To provide a fully automated distributed pipeline for large-scale structural and functional annotation of all major proteomes via the use of cutting-edge computer GRID technologies".

Search space modified to include HMM profile based hits (using HMMer) for regions left unannotated by PSI-BLAST and RPS-BLAST (PSSM profile based methods). The SCOP domain database has been updated to version 1.69

The underlying database has been updated to provide greater stability and increased spped for the provision of results. Hopefully, this will be the last major down time for a while.

The 3D-GENOMICS database is currently down. We are looking into this and hope to have the problem rectified soon.

The 3D-GENOMICS database is back up after database errors were fixed.

The 3D-GENOMICS database is currently down. We are looking into this and hope to have the problem rectified soon.

Homology models are now available for the protein sequences of 13 genomes:

• Homo sapiens
• Saccharomyces cerevisiae
• Aeropyrum pernix
• Archaeoglobus fulgidus
• Bacillus subtilis
• Methanococcus jannaschii
• Aquifex aeolicus
• Chlamydia trachomatis
• Escherichia coli K12
• Haemophilus influenzae
• Listeria innocua
• Mycobacterium tuberculosis H37Rv
• Mycoplasma genitalium

See this page for an example. The models are built from alignments to homologous PDB/SCOP regions. Each model can be downloaded as a PDB file or viewed using Jmol (requires Java) or RasMol (via a plugin).

Please use the 'Query Database' link above to search for sequences of interest.

The database has been updated with 173 genomes (see Methods and data versions for full list of genomes). Each genome has been re-annotated with the latest software versions. Database querying and results pages have also undergone some changes to increase usability.

The 3D-GENOMICS database is back up after a software update caused problems with access.

The 3D-GENOMICS database is currently down. We are looking into this and hope to have the problem rectified soon.

New data has been uploaded for all of the 93 genomes included in the database. The Annotation overview option in Query database -> Top-down analysis presents the new figures for the state of annotations for each genome.

We are experiencing problems with the 3D-GENOMICS database this afternoon. We're looking into this and hope to have the problem rectified soon.

Querying the database with an amino acid sequence will now return all of the closest matching sequences if an exact match cannot be found. The sequences are presented in descending order of similarity to the query sequence.

The problem with database access has been solved.

We are experiencing problems with the 3D-GENOMICS database. We're looking into this and hope to have the problem rectified soon.

The database has been updated so that queries should now be returned faster than before.

The database is being updated so cannot be used currently. This is anticipated to last until tomorrow morning.

Regions determined as part of the COG (Clusters of Orthologous Groups) phylogenetic classification have been added to the database. Presently, coverage is available for 66 genomes. More information about this database and a list of the covered genomes can be found on the COG website at the NCBI.

The 3D-GENOMICS database has undergone a large expansion, now encompassing >100 genomes . In addition, a much higher throughput for the annotation procedure has been achieved thanks to the use of the facilities at the London e-Science centre .

The user interface to 3D-GENOMICS has been reworked to allow easier access to the database.