Imperial College London
Alternate

ProfessorMichaelSternberg

Faculty of Natural Sciences, Department of Life Sciences

Director, Systems Biology and Bioinformatics Centre
 
 
 
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Contact

 

+44 (0)20 7594 5212m.sternberg Website

 
 
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Location

 

306Sir Ernst Chain BuildingSouth Kensington Campus

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Summary

 

Publications

Citation

BibTex format

@article{Sillitoe:2019:nar/gkz967,
author = {Sillitoe, I and Andreeva, A and Blundell, TL and Buchan, DWA and Finn, RD and Gough, J and Jones, D and Kelley, LA and Paysan-Lafosse, T and Lam, SD and Murzin, AG and Pandurangan, AP and Salazar, GA and Skwark, MJ and Sternberg, MJE and Velankar, S and Orengo, C},
doi = {nar/gkz967},
journal = {Nucleic Acids Research},
pages = {D314--D319},
title = {Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation},
url = {http://dx.doi.org/10.1093/nar/gkz967},
volume = {48},
year = {2019}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - Genome3D (https://www.genome3d.eu) is a freely available resource that provides consensus structural annotations for representative protein sequences taken from a selection of model organisms. Since the last NAR update in 2015, the method of data submission has been overhauled, with annotations now being 'pushed' to the database via an API. As a result, contributing groups are now able to manage their own structural annotations, making the resource more flexible and maintainable. The new submission protocol brings a number of additional benefits including: providing instant validation of data and avoiding the requirement to synchronise releases between resources. It also makes it possible to implement the submission of these structural annotations as an automated part of existing internal workflows. In turn, these improvements facilitate Genome3D being opened up to new prediction algorithms and groups. For the latest release of Genome3D (v2.1), the underlying dataset of sequences used as prediction targets has been updated using the latest reference proteomes available in UniProtKB. A number of new reference proteomes have also been added of particular interest to the wider scientific community: cow, pig, wheat and mycobacterium tuberculosis. These additions, along with improvements to the underlying predictions from contributing resources, has ensured that the number of annotations in Genome3D has nearly doubled since the last NAR update article. The new API has also been used to facilitate the dissemination of Genome3D data into InterPro, thereby widening the visibility of both the annotation data and annotation algorithms.
AU  - Sillitoe,I
AU  - Andreeva,A
AU  - Blundell,TL
AU  - Buchan,DWA
AU  - Finn,RD
AU  - Gough,J
AU  - Jones,D
AU  - Kelley,LA
AU  - Paysan-Lafosse,T
AU  - Lam,SD
AU  - Murzin,AG
AU  - Pandurangan,AP
AU  - Salazar,GA
AU  - Skwark,MJ
AU  - Sternberg,MJE
AU  - Velankar,S
AU  - Orengo,C
DO  - nar/gkz967
EP  - 319
PY  - 2019///
SN  - 0305-1048
SP  - 314
TI  - Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation
T2  - Nucleic Acids Research
UR  - http://dx.doi.org/10.1093/nar/gkz967
UR  - https://www.ncbi.nlm.nih.gov/pubmed/31733063
UR  - https://academic.oup.com/nar/article/48/D1/D314/5626529
UR  - http://hdl.handle.net/10044/1/75224
VL  - 48
ER  -
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