Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains

Title: Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains
Author(s): Lewis, TE
Sillitoe, I
Andreeva, A
Blundell, TL
Buchan, DW
Chothia, C
Cuff, A
Dana, JM
Filippis, I
Gough, J
Hunter, S
Jones, DT
Kelley, LA
Kleywegt, GJ
Minneci, F
Mitchell, A
Murzin, AG
Ochoa-Montano, B
Rackham, OJ
Smith, J
Sternberg, MJ
Velankar, S
Yeats, C
Orengo, C
Item Type: Journal Article
Abstract: Genome3D, available at http://www.genome3d.eu, is a new collaborative project that integrates UK-based structural resources to provide a unique perspective on sequence-structure-function relationships. Leading structure prediction resources (DomSerf, FUGUE, Gene3D, pDomTHREADER, Phyre and SUPERFAMILY) provide annotations for UniProt sequences to indicate the locations of structural domains (structural annotations) and their 3D structures (structural models). Structural annotations and 3D model predictions are currently available for three model genomes (Homo sapiens, E. coli and baker's yeast), and the project will extend to other genomes in the near future. As these resources exploit different strategies for predicting structures, the main aim of Genome3D is to enable comparisons between all the resources so that biologists can see where predictions agree and are therefore more trusted. Furthermore, as these methods differ in whether they build their predictions using CATH or SCOP, Genome3D also contains the first official mapping between these two databases. This has identified pairs of similar superfamilies from the two resources at various degrees of consensus (532 bronze pairs, 527 silver pairs and 370 gold pairs).
Publication Date: 1-Jan-2013
URI: http://hdl.handle.net/10044/1/56809
DOI: https://dx.doi.org/10.1093/nar/gks1266
ISSN: 1362-4962
Start Page: D499
End Page: D507
Journal / Book Title: Nucleic Acids Res
Volume: 41
Sponsor/Funder: Biotechnology and Biological Sciences Research Council (BBSRC)
Biotechnology and Biological Sciences Research Council (BBSRC)
Funder's Grant Number: BB/I025271/1
BB/J019240/1
Copyright Statement: © The Author(s) 2012. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com.
Keywords: Science & Technology
Life Sciences & Biomedicine
Biochemistry & Molecular Biology
HIDDEN MARKOV-MODELS
PROTEIN STRUCTURES
FOLD RECOGNITION
ALGORITHM
SUPERFAMILY
HOMOLOGY
DATABASE
ALIGNMENTS
ASSIGNMENT
PHYRE
Databases, Protein
Genomics
Humans
Internet
Molecular Sequence Annotation
Protein Structure, Tertiary
Proteins
Software
Humans
Proteins
Genomics
Protein Structure, Tertiary
Internet
Software
Databases, Protein
Molecular Sequence Annotation
05 Environmental Sciences
06 Biological Sciences
08 Information And Computing Sciences
Developmental Biology
Appears in Collections:Faculty of Natural Sciences



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