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Genome3D: exploiting structure to help users understand their sequences

Genome3D: exploiting structure to help users understand their sequences
Genome3D: exploiting structure to help users understand their sequences

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.

Algorithms, Databases, Protein, Genomics, Internet, Models, Molecular, Molecular Sequence Annotation, Protein Structure, Tertiary/genetics, Sequence Analysis, Protein
0305-1048
D382-D386
Lewis, Tony E.
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Sillitoe, Ian
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Andreeva, Antonina
ecb88dab-8c3e-4def-82c5-83d1147f5801
Blundell, Tom L.
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Buchan, Daniel W.A.
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Chothia, Cyrus
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Cozzetto, Domenico
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Dana, José M
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Filippis, Ioannis
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Gough, Julian
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Jones, David T.
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Kelley, Lawrence A.
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Kleywegt, Gerard J.
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Minneci, Federico
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Mistry, Jaina
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Murzin, Alexey G.
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Ochoa-Montaño, Bernardo
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Oates, Matt E.
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Punta, Marco
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Rackham, Owen J.L.
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Stahlhacke, Jonathan
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Sternberg, Michael J.E.
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Velankar, Sameer
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Orengo, Christine
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Lewis, Tony E.
a2f720ba-b410-48b0-b4aa-ed3ac381f77d
Sillitoe, Ian
7211e2a9-6725-412d-9042-fd7704239ca1
Andreeva, Antonina
ecb88dab-8c3e-4def-82c5-83d1147f5801
Blundell, Tom L.
c561b8e8-13bc-4403-b31e-46bda6630d5d
Buchan, Daniel W.A.
562262f0-99c6-420f-80e2-5e902f5f15bf
Chothia, Cyrus
63accbe7-0f8d-4b33-9f28-c7cfd53d9efa
Cozzetto, Domenico
2f680e8e-a6f2-405e-9e26-7b106d857d61
Dana, José M
04ce15e8-8d57-456e-8507-77788800f4fc
Filippis, Ioannis
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Gough, Julian
019ed039-9fd4-45d6-aa7a-12a8fcf7245c
Jones, David T.
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Kelley, Lawrence A.
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Kleywegt, Gerard J.
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Minneci, Federico
23daff3d-f935-482d-addb-d52a991a40bc
Mistry, Jaina
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Murzin, Alexey G.
6adacb3d-c3a9-43bc-b647-f48d5d2f769c
Ochoa-Montaño, Bernardo
e5500b10-c1cd-41c9-a980-8112b7dc20ff
Oates, Matt E.
c90996e2-2ae0-4784-9633-a1db986b1831
Punta, Marco
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Rackham, Owen J.L.
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Stahlhacke, Jonathan
2e55897b-f50f-45e9-90cf-b538adf19d2f
Sternberg, Michael J.E.
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Velankar, Sameer
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Orengo, Christine
f75f273c-e5ca-42df-851e-5e9ababb9494

Lewis, Tony E., Sillitoe, Ian, Andreeva, Antonina, Blundell, Tom L., Buchan, Daniel W.A., Chothia, Cyrus, Cozzetto, Domenico, Dana, José M, Filippis, Ioannis, Gough, Julian, Jones, David T., Kelley, Lawrence A., Kleywegt, Gerard J., Minneci, Federico, Mistry, Jaina, Murzin, Alexey G., Ochoa-Montaño, Bernardo, Oates, Matt E., Punta, Marco, Rackham, Owen J.L., Stahlhacke, Jonathan, Sternberg, Michael J.E., Velankar, Sameer and Orengo, Christine (2015) Genome3D: exploiting structure to help users understand their sequences. Nucleic Acids Research, 43 (D1), D382-D386. (doi:10.1093/nar/gku973).

Record type: Article

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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More information

Accepted/In Press date: 2 October 2014
e-pub ahead of print date: 27 October 2014
Published date: January 2015
Additional Information: © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
Keywords: Algorithms, Databases, Protein, Genomics, Internet, Models, Molecular, Molecular Sequence Annotation, Protein Structure, Tertiary/genetics, Sequence Analysis, Protein

Identifiers

Local EPrints ID: 446732
URI: http://eprints.soton.ac.uk/id/eprint/446732
ISSN: 0305-1048
PURE UUID: 1a8cd6ec-1291-44eb-ac73-2074cc12373c
ORCID for Owen J.L. Rackham: ORCID iD orcid.org/0000-0002-4390-0872

Catalogue record

Date deposited: 19 Feb 2021 17:31
Last modified: 10 Jun 2022 01:55

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Contributors

Author: Tony E. Lewis
Author: Ian Sillitoe
Author: Antonina Andreeva
Author: Tom L. Blundell
Author: Daniel W.A. Buchan
Author: Cyrus Chothia
Author: Domenico Cozzetto
Author: José M Dana
Author: Ioannis Filippis
Author: Julian Gough
Author: David T. Jones
Author: Lawrence A. Kelley
Author: Gerard J. Kleywegt
Author: Federico Minneci
Author: Jaina Mistry
Author: Alexey G. Murzin
Author: Bernardo Ochoa-Montaño
Author: Matt E. Oates
Author: Marco Punta
Author: Jonathan Stahlhacke
Author: Michael J.E. Sternberg
Author: Sameer Velankar
Author: Christine Orengo

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