Genome3D
Genome3D is a resource that provides structural annotation and 3D models of genomes of model organisms such as human, yeast and E.coli. The database can be used to predict protein structures that have not yet been identified. Genome3D uses structural classification data from several UK-based resources including CATH and SCOP.
Description
More detailed information about this field from each metasource.
Genome3D is a resource that provides structural annotation and 3D models of genomes of model organisms such as human, yeast and E.coli. The database can be used to predict protein structures that have not yet been identified. Genome3D uses structural classification data from several UK-based resources including CATH and SCOP.
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Domain structure predictions and 3D models for proteins from model genomes
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://genome3d.euWebpage
More detailed information about this field from each metasource.
http://genome3d.eu
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://www.genome3d.eu
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Publications:
Publications
More detailed information about this field from each metasource.
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains
PMID: 23203986
metasource: Fairsharing.org
version: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Genome3D: exploiting structure to help users understand their sequences
PMID: 25348407
metasource: Fairsharing.org
version: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gku973
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains
PMID: 23203986
metasource: Fairsharing.org
version: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Genome3D: exploiting structure to help users understand their sequences
PMID: 25348407
metasource: Fairsharing.org
version: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/gku973
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains
PubMed citations: 30.
30 articles citing: Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains
Ligand-based virtual screening, molecular docking, and molecular dynamics of eugenol analogs as potential acetylcholinesterase inhibitors with biological activity against Spodoptera frugiperda. PMID:34529209
ProtCHOIR: a tool for proteome-scale generation of homo-oligomers. PMID:34015821
Protein domain identification methods and online resources. PMID:33680357
Molecular replacement using structure predictions from databases. PMID:31793899
Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation. PMID:31733063
Mabellini: a genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus. PMID:31681953
Identification and validation of a novel panel of Plasmodium knowlesi biomarkers of serological exposure. PMID:29902183
Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis. PMID:29769048
Guidelines for the successful generation of protein-ligand complex crystals. PMID:28177304
Time, space, and disorder in the expanding proteome universe. PMID:28145059
SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins - extended Database. PMID:27914894
Lessons from making the Structural Classification of Proteins (SCOP) and their implications for protein structure modelling. PMID:27284063
The history of the CATH structural classification of protein domains. PMID:26253692
Anatomy of BioJS, an open source community for the life sciences. PMID:26153621
The Phyre2 web portal for protein modeling, prediction and analysis. PMID:25950237
CHOPIN: a web resource for the structural and functional proteome of Mycobacterium tuberculosis. PMID:25833954
A hybrid method for identification of structural domains. PMID:25503992
Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. PMID:25503938
Protein structure annotation resources. PMID:25502191
Open source libraries and frameworks for biological data visualisation: a guide for developers. PMID:25475079
The InterPro protein families database: the classification resource after 15 years. PMID:25428371
The SUPERFAMILY 1.75 database in 2014: a doubling of data. PMID:25414345
Genome3D: exploiting structure to help users understand their sequences. PMID:25348407
BioJS: an open source standard for biological visualisation - its status in 2014. PMID:25075290
SuSPect: enhanced prediction of single amino acid variant (SAV) phenotype using network features. PMID:24810707
Classification of intrinsically disordered regions and proteins. PMID:24773235
Revisiting amino acid substitution matrices for identifying distantly related proteins. PMID:24281694
Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis. PMID:24270792
Cluster and fold stability of E. coli ISC-type ferredoxin. PMID:24265733
The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection. PMID:23203983 -
Genome3D: exploiting structure to help users understand their sequences
PubMed citations: 20.
20 articles citing: Genome3D: exploiting structure to help users understand their sequences
Somatic Mutations Detected in Parkinson Disease Could Affect Genes With a Role in Synaptic and Neuronal Processes. PMID:35821807
Germline biallelic mutation affecting the transcription factor Helios causes pleiotropic defects of immunity. PMID:34826259
Cosolvent and Dynamic Effects in Binding Pocket Search by Docking Simulations. PMID:34730967
ProtCHOIR: a tool for proteome-scale generation of homo-oligomers. PMID:34015821
On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction. PMID:33937764
MSA-Regularized Protein Sequence Transformer toward Predicting Genome-Wide Chemical-Protein Interactions: Application to GPCRome Deorphanization. PMID:33757283
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). PMID:32566135
Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation. PMID:31733063
Mabellini: a genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus. PMID:31681953
Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints. PMID:31484923
FunFam protein families improve residue level molecular function prediction. PMID:31319797
The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver. PMID:30445555
Ensemble Docking in Drug Discovery. PMID:29606412
An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences. PMID:28777078
Challenges for visualizing three-dimensional data in genomic browsers. PMID:28771695
Effects of ADAMTS14 genetic polymorphism and cigarette smoking on the clinicopathologic development of hepatocellular carcinoma. PMID:28231306
The SWISS-MODEL Repository-new features and functionality. PMID:27899672
The archiving and dissemination of biological structure data. PMID:27450113
Partial protein domains: evolutionary insights and bioinformatics challenges. PMID:25986583
The 2015 Nucleic Acids Research Database Issue and molecular biology database collection. PMID:25593347 - http://dx.doi.org/10.1093/nar/gku973
Tags:
Tags
More detailed information about this field from each metasource.
annotation
metasource: Fairsharing.org
version: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
classification
metasource: Fairsharing.org
version: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
genome
metasource: Fairsharing.org
version: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
genome annotation
metasource: Fairsharing.org
version: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
model organism
metasource: Fairsharing.org
version: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
molecular structure
metasource: Fairsharing.org
version: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein domain
metasource: Fairsharing.org
version: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein structure
metasource: Fairsharing.org
version: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
polypeptide_region
metasource: Fairsharing.org
version: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
structure databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Tags
More detailed information about this field from each metasource.
annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
classification
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
genome
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
genome annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
model organism
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
molecular structure
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein domain
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein structure
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
polypeptide_region
metasource: Fairsharing.orgversion: FAIRsharing.org: Genome3D; Genome3D; DOI: https://doi.org/10.25504/FAIRsharing.VW2yBw; Last edited: March 19, 2021, 1 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
structure databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
classification genome genome annotation model organism molecular structure protein domain protein structure polypeptide region structure
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