ArticleNucleic acids research2016
Gene3D: expanding the utility of domain assignments.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 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
38 citing papers in PubMed.
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- Dominance of recombinant DWV genomes with changing viral landscapes as revealed in national US honey bee and varroa mite survey.Communications biology · 2024Article
- Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet.Genome biology · 2024Article
- Protein length distribution is remarkably uniform across the tree of life.Genome biology · 2023Article
- Genomic basis of the giga-chromosomes and giga-genome of tree peony Paeonia ostii.Nature communications · 2022Article
- I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction.Nature protocols · 2022Review
- Gene Mining for Conserved, Non-Annotated Proteins ofJournal of fungi (Basel, Switzerland) · 2021Article
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- An Update on MRMAssayDB: A Comprehensive Resource for Targeted Proteomics Assays in the Community.Journal of proteome research · 2021Article
- Biological impact of mutually exclusive exon switching.PLoS computational biology · 2021Article
- OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more.Nucleic acids research · 2021Article
- Schistosomiasis Drug Discovery in the Era of Automation and Artificial Intelligence.Frontiers in immunology · 2021Review
- Progressive and accurate assembly of multi-domain protein structures from cryo-EM density maps.bioRxiv : the preprint server for biology · 2020Article
- SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals.Scientific reports · 2020Article
- Protein functional annotation of simultaneously improved stability, accuracy and false discovery rate achieved by a sequence-based deep learning.Briefings in bioinformatics · 2020Article
- A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina.Nature communications · 2020Article
- Protein Stability in Titan's Subsurface Water Ocean.Astrobiology · 2020Article
- Article
- Assembling multidomain protein structures through analogous global structural alignments.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Gene3D http://gene3d.biochem.ucl.ac.uk is a database of domain annotations of Ensembl and UniProtKB protein sequences. Domains are predicted using a library of profile HMMs representing 2737 CATH superfamilies. Gene3D has previously featured in the Database issue of NAR and here we report updates to the website and database. The current Gene3D (v14) release has expanded its domain assignments to ∼ 20,000 cellular genomes and over 43 million unique protein sequences, more than doubling the number of protein sequences since our last publication. Amongst other updates, we have improved our Functional Family annotation method. We have also improved the quality and coverage of our 3D homology modelling pipeline of predicted CATH domains. Additionally, the structural models have been expanded to include an extra model organism (Drosophila melanogaster). We also document a number of additional visualization tools in the Gene3D website.
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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.