Genome3D: exploiting structure to help users understand their sequences
By Tony E. Lewis, Ian Sillitoe, Antonina Andreeva, Tom L. Blundell, Daniel W. A. Buchan, Cyrus Chothia, Domenico Cozzetto, J. M. Dana, Ioannis Filippis, Julian Gough and 14 more. 2014
47 citations recorded by the source corpus.
Genome3D (http://www.genome3d.eu) is a collaborative resource that provides predicted domain annotations and structural models for key sequences. Since introducing Genome3D in a previous NAR paper, we have substantially extended and improved the resource. We have annotated representatives from Pfam families to improve coverage of diverse sequences and added a fast sequence search to the website to allow users to find Genome3D-annotated sequences similar to their own. We have improved and extended the Genome3D data, enlarging the source data set from three model organisms to 10, and adding VIVACE, a resource new to Genome3D. We have analysed and updated Genome3D's SCOP/CATH mapping. Finally, we have improved the superposition tools, which now give users a more powerful interface for investigating similarities and differences between structural models.
Subfields: Molecular Biology
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In Molecular Biology
- Torsten Schwede
- Joe G. Greener
- Shaun M. Kandathil
- Lorenza Bordoli
- David T. Jones
- Yang Zhang
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- Andrew M. Waterhouse
Citations in the corpus
- The SWISS-MODEL Repository—new features and functionality (2016, background): “The computational structural biology community has a long tradition of providing protein model databases such as the Genomic Threading Database (4,5), ModBase (6), Genome 3D (7), GPCRdb (8) and SWISS-MODEL Repository (SMR) (9) as well as protein functional annotation databases such as Superfamily (1”
- Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints (2018, background): “Also, this efficiency means that we will be easily able to maintain a continuously updated set of de novo modelled Pfam domains, which will be distributed via the Genome3D resource [29].”