ArticleNucleic acids research2013
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
32 citing papers in PubMed.
- Assignment of structural domains in proteins using diffusion kernels on graphs.BMC bioinformatics · 2022Article
- Ligand-based virtual screening, molecular docking, and molecular dynamics of eugenol analogs as potential acetylcholinesterase inhibitors with biological activity against Spodoptera frugiperda.Molecular diversity · 2022Article
- ProtCHOIR: a tool for proteome-scale generation of homo-oligomers.Briefings in bioinformatics · 2021Article
- Protein domain identification methods and online resources.Computational and structural biotechnology journal · 2021Review
- Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation.Nucleic acids research · 2020Article
- Molecular replacement using structure predictions from databases.Acta crystallographica. Section D, Structural biology · 2019Article
- Mabellini: a genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus.Database : the journal of biological databases and curation · 2019Article
- Identification and validation of a novel panel of Plasmodium knowlesi biomarkers of serological exposure.PLoS neglected tropical diseases · 2018Article
- Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis.BMC structural biology · 2018Article
- Time, space, and disorder in the expanding proteome universe.Proteomics · 2017Article
- SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins - extended Database.Journal of molecular biology · 2017Article
- Guidelines for the successful generation of protein-ligand complex crystals.Acta crystallographica. Section D, Structural biology · 2017Review
- Lessons from making the Structural Classification of Proteins (SCOP) and their implications for protein structure modelling.Biochemical Society transactions · 2016Review
- Review
- Article
- The Phyre2 web portal for protein modeling, prediction and analysis.Nature protocols · 2015Article
- Open source libraries and frameworks for biological data visualisation: a guide for developers.Proteomics · 2015Review
- Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently.Chemical Society reviews · 2015Review
- The SUPERFAMILY 1.75 database in 2014: a doubling of data.Nucleic acids research · 2015Article
- CHOPIN: a web resource for the structural and functional proteome of Mycobacterium tuberculosis.Database : the journal of biological databases and curation · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
24 authors.
Funding
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).
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.