ArticleNucleic acids research2012
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 68 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
68 citing papers in PubMed.
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- Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling.Nature microbiology · 2026Article
- DynaRepo: the repository of macromolecular conformational dynamics.Nucleic acids research · 2026Article
- Chromosome-Level Genome Assembly of the Loach Goby Rhyacichthys aspro Offers Insights Into Gobioidei Evolution.Molecular ecology resources · 2025Article
- LRRK2 rare-variant per-domain genetic burden in Parkinson's Disease: association confined to the kinase domain.NPJ Parkinson's disease · 2025Article
- A chromosome-level genome assembly of Meteorus pulchricornis Wesmael (Hymenoptera: Braconidae).Scientific data · 2025Article
- Dominance of recombinant DWV genomes with changing viral landscapes as revealed in national US honey bee and varroa mite survey.Communications biology · 2024Article
- Exploring structural diversity across the protein universe with The Encyclopedia of Domains.Science (New York, N.Y.) · 2024Article
- Searching for new plastic-degrading enzymes from the plastisphere of alpine soils using a metagenomic mining approach.PloS one · 2024Article
- Navigating the archaeal frontier: insights and projections from bioinformatic pipelines.Frontiers in microbiology · 2024Article
- ProCogGraph: a graph-based mapping of cognate ligand domain interactions.Bioinformatics advances · 2024Article
- Functional domains ofFrontiers in microbiology · 2024Article
- Article
- Chromosome-level genome assembly of Microplitis manilae Ashmead, 1904 (Hymenoptera: Braconidae).Scientific data · 2023Article
- In Silico Characterization of the Secretome of the Fungal PathogenJournal of fungi (Basel, Switzerland) · 2023Article
- Differences in pseudogene evolution contributed to the contrasting flavors of turnip and Chiifu, two Brassica rapa subspecies.Plant communications · 2023Article
- The difficulty of aligning intrinsically disordered protein sequences as assessed by conservation and phylogeny.PloS one · 2023Article
- Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes.Frontiers in artificial intelligence · 2023Article
- De novo genome assembly and annotation of Holothuria scabra (Jaeger, 1833) from nanopore sequencing reads.Genes & genomics · 2022Article
8 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
7 authors.
Funding
Abstract
Gene3D http://gene3d.biochem.ucl.ac.uk is a comprehensive database of protein domain assignments for sequences from the major sequence databases. Domains are directly mapped from structures in the CATH database or predicted using a library of representative profile HMMs derived from CATH superfamilies. As previously described, Gene3D integrates many other protein family and function databases. These facilitate complex associations of molecular function, structure and evolution. Gene3D now includes a domain functional family (FunFam) level below the homologous superfamily level assignments. Additions have also been made to the interaction data. More significantly, to help with the visualization and interpretation of multi-genome scale data sets, we have developed a new, revamped website. Searching has been simplified with more sophisticated filtering of results, along with new tools based on Cytoscape Web, for visualizing protein-protein interaction networks, differences in domain composition between genomes and the taxonomic distribution of individual superfamilies.
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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.