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. 2015 Jan;43(Database issue):D382-6.
doi: 10.1093/nar/gku973. Epub 2014 Oct 27.

Genome3D: exploiting structure to help users understand their sequences

Tony E Lewis  1 , Ian Sillitoe  2 , Antonina Andreeva  3 , Tom L Blundell  4 , Daniel W A Buchan  5 , Cyrus Chothia  3 , Domenico Cozzetto  5 , José M Dana  6 , Ioannis Filippis  7 , Julian Gough  8 , David T Jones  9 , Lawrence A Kelley  7 , Gerard J Kleywegt  6 , Federico Minneci  5 , Jaina Mistry  6 , Alexey G Murzin  3 , Bernardo Ochoa-Montaño  4 , Matt E Oates  8 , Marco Punta  6 , Owen J L Rackham  10 , Jonathan Stahlhacke  8 , Michael J E Sternberg  7 , Sameer Velankar  6 , Christine Orengo  1
Affiliations

Genome3D: exploiting structure to help users understand their sequences

Tony E Lewis et al. Nucleic Acids Res. 2015 Jan.

Abstract

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.

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Figures

Figure 1.
Figure 1.
Coverage of UniProt sequences in each genome by the number of resources providing at least one domain annotation for the sequence. ‘Pfam (single domain)’ denotes the new data set of sequences representing Pfam families and ‘Pfam (architecture)’ denotes the extra data set of sequences representing the Pfam multi-domain architectures, as discussed in the main text.
Figure 2.
Figure 2.
Coverage of UniProt sequences in each genome by the number of resources providing at least one structural model for the sequence. ‘Pfam (single domain)’ denotes the new data set of sequences representing Pfam families, as discussed in the main text.
Figure 3.
Figure 3.
PyMOL downloads of Genome3D superpositions now include black alignment lines that connect the locations in which the different structural models place the same residue from the source sequence. These images show a superposition of four resources’ structural models of OR5AL1 (UniProt accession: P0C617) with the alignment lines displayed. In (b), the models predict two structurally similar helices but differ about where to locate the source sequence's residues on the yellow helix at the bottom.
See this image and copyright information in PMC

References

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