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Genome3D specifications


Unique identifier OMICS_06084
Name Genome3D
Restrictions to use None
Maintained Yes


  • Primates
    • Homo sapiens

Publication for Genome3D

Genome3D citations


An overview of comparative modelling and resources dedicated to large scale modelling of genome sequences

Acta Crystallogr D Struct Biol
PMCID: 5571743
PMID: 28777078
DOI: 10.1107/S2059798317008920

[…] Genome3D (Lewis et al., 2015) is a UK-based collaborative project to annotate genome sequences with structural information. The participating partners includes Gene3D (Lam et al., 2016), SUPERFAMILY ( […]


Analysis methods for studying the 3D architecture of the genome

Genome Biol
PMCID: 4556012
PMID: 26328929
DOI: 10.1186/s13059-015-0745-7

[…] features such as domain calls, peak calls from HiCCUPS, and CTCF binding sites []. Several tools are currently under development for visualization of three-dimensional models of chromatin, including Genome3D [] and TADkit []. […]


Open source libraries and frameworks for biological data visualisation: A guide for developers

PMCID: 4409855
PMID: 25475079
DOI: 10.1002/pmic.201400377

[…] formatics projects. Recent examples include: (i) PIQMIe [] (, a web server for performing semi-quantitative proteomics data management and analysis; (ii) Genome3D [], a UK collaborative project created to annotate genomic sequences with predicted 3D structures based on the SCOP (Structural Classification of Proteins) and CATH (Class, Architecture, Topo […]


Anatomy of BioJS, an open source community for the life sciences

PMCID: 4495654
PMID: 26153621
DOI: 10.7554/eLife.07009

[…] ts, such as BioGem (). Several recognized projects and institutions have already shown commitment to BioJS by utilizing and developing components: examples of this include PredictProtein (), CATH (), Genome3D (), Reactome (), Expression Atlas (), Ensembl (), InterMine (), PolyMarker () and the TGAC Browser ( […]


Identification and characterization of the nitrate assimilation genes in the isolate of Streptomyces griseorubens JSD 1

Microb Cell Fact
PMCID: 4272520
PMID: 25492123
DOI: 10.1186/s12934-014-0174-4

[…] Putative 3D structures of these analyzed proteins were predicted by online program PHYRE 2.0 Server ( in the intensive mode []. Protein sequences were used to search against the ExPDB template library. Sequences with the most identities were used for model generation. All 3D images were […]


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

Nucleic Acids Res
PMCID: 3531217
PMID: 23203986
DOI: 10.1093/nar/gks1266

[…] into their respective families using a hybrid pairwise-profile method ().The confidence scores produced by SUPERFAMILY are per-sequence E-values, and only high-confidence predictions are provided to Genome3D, with an threshold of E < 0.0001, although higher coverage (lower confidence) predictions can be explored via the SUPERFAMILY website. A byproduct of the hybrid sub-family classification proc […]


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Genome3D institution(s)
Institute of Structural and Molecular Biology, UCL, London, UK; MRC Laboratory of Molecular Biology, Hills Road, Cambridge, UK; Department of Biochemistry, University of Cambridge, Cambridge, UK; Department of Computer Science, UCL, London, UK; European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK; Centre for Bioinformatics, Department of Life Sciences, Imperial College London, London, UK; Department of Computer Science, University of Bristol, Merchant Venturers Building, Woodland Road, Bristol, UK; European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK; MRC Clinical Sciences Centre, Hammersmith Hospital Campus, London, UK

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