ArticleNucleic acids research2010
Gene3D: merging structure and function for a Thousand genomes.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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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.
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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
30 citing papers in PubMed.
- Genome-wide prediction of cloned disease resistance homologues across the Oryza genus.The plant genome · 2026Article
- Decoding the human PBMC isonome: isoform-level resolution with single-cell long-read transcriptomics.Frontiers in genetics · 2026Article
- Halotolerant bacterial endophyteFrontiers in plant science · 2024Article
- A Comparison of Differential Gene Expression in Response to the Onset of Water Stress Between Three Hybrid Brachiaria Genotypes.Frontiers in plant science · 2021Article
- Article
- Structural and Functional View of Polypharmacology.Scientific reports · 2017Article
- Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains.Traffic (Copenhagen, Denmark) · 2016Article
- PinSnps: structural and functional analysis of SNPs in the context of protein interaction networks.Bioinformatics (Oxford, England) · 2016Article
- In silico Identification and Taxonomic Distribution of Plant Class C GH9 Endoglucanases.Frontiers in plant science · 2016Article
- One origin for metallo-β-lactamase activity, or two? An investigation assessing a diverse set of reconstructed ancestral sequences based on a sample of phylogenetic trees.Journal of molecular evolution · 2014Article
- SeqDepot: streamlined database of biological sequences and precomputed features.Bioinformatics (Oxford, England) · 2014Article
- Prediction of detailed enzyme functions and identification of specificity determining residues by random forests.PloS one · 2014Article
- Evolutionary history of the TBP-domain superfamily.Nucleic acids research · 2013Article
- New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.Nucleic acids research · 2013Article
- Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.Nucleic acids research · 2013Article
- Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes.PLoS computational biology · 2013Article
- Article
- Metagenomic analysis: the challenge of the data bonanza.Briefings in bioinformatics · 2012Review
- GFam: a platform for automatic annotation of gene families.Nucleic acids research · 2012Article
- Distribution and prediction of catalytic domains in 2-oxoglutarate dependent dioxygenases.BMC research notes · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Over the last 2 years the Gene3D resource has been significantly improved, and is now more accurate and with a much richer interactive display via the Gene3D website (http://gene3d.biochem.ucl.ac.uk/). Gene3D provides accurate structural domain family assignments for over 1100 genomes and nearly 10,000,000 proteins. A hidden Markov model library, constructed from the manually curated CATH structural domain hierarchy, is used to search UniProt, RefSeq and Ensembl protein sequences. The resulting matches are refined into simple multi-domain architectures using a recently developed in-house algorithm, DomainFinder 3 (available at: ftp://ftp.biochem.ucl.ac.uk/pub/gene3d_data/DomainFinder3/). The domain assignments are integrated with multiple external protein function descriptions (e.g. Gene Ontology and KEGG), structural annotations (e.g. coiled coils, disordered regions and sequence polymorphisms) and family resources (e.g. Pfam and eggNog) and displayed on the Gene3D website. The website allows users to view descriptions for both single proteins and genes and large protein sets, such as superfamilies or genomes. Subsets can then be selected for detailed investigation or associated functions and interactions can be used to expand explorations to new proteins. Gene3D also provides a set of services, including an interactive genome coverage graph visualizer, DAS annotation resources, sequence search facilities and SOAP services.
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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.