Gene3D: Extensive prediction of globular domains in proteins

Abstract Gene3D (http://gene3d.biochem.ucl.ac.uk) is a database of globular domain annotations for millions of available protein sequences. Gene3D has previously featured in the Database issue of NAR and here we report a significant update to the Gene3D database. The current release, Gene3D v16, has significantly expanded its domain coverage over the previous version and now contains over 95 million domain assignments. We also report a new method for dealing with complex domain architectures that exist in Gene3D, arising from discontinuous domains. Amongst other updates, we have added visualization tools for exploring domain annotations in the context of other sequence features and in gene families. We also provide web-pages to visualize other domain families that co-occur with a given query domain family.

• Publication year

  2017

• Venue

  Nucleic Acids Res.

• Publication date

  2017-11-03

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/nar/gkx1069PMID 29112716PMCID 5753370
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• ProtVista: visualization of protein sequence annotations

  2017cited by this paper
• PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization

  2017cited by this paper
• TP53 copy number expansion is associated with the evolution of increased body size and an enhanced DNA damage response in elephants

  2016cited by this paper
• Ensembl comparative genomics resources

  2016cited by this paper
• Query-seeded iterative sequence similarity searching improves selectivity 5–20-fold

  2016cited by this paper
• Correction: TP53 copy number expansion is associated with the evolution of increased body size and an enhanced DNA damage response in elephants

  2016cited by this paper
• UniProt: the universal protein knowledgebase

  2016cited by this paper
• An expanded evaluation of protein function prediction methods shows an improvement in accuracy

  2016cited by this paper
• The revolution will not be crystallized: a new method sweeps through structural biology

  2015cited by this paper
• Panoramic view of a superfamily of phosphatases through substrate profiling

  2015cited by this paper
• Functional classification of CATH superfamilies: a domain-based approach for protein function annotation

  2015cited by this paper
• Gene3D: expanding the utility of domain assignments

  2015cited by this paper
• TP53 copy number expansion is associated with the evolution of increased body size and an enhanced DNA damage response in elephants

  2015cited by this paper
• CATH: comprehensive structural and functional annotations for genome sequences

  2014cited by this paper
• SIFTS: Structure Integration with Function, Taxonomy and Sequences resource

  2012cited by this paper
• Accelerated Profile HMM Searches

  2011cited by this paper
• A fast and automated solution for accurately resolving protein domain architectures

  2010cited by this paper
• UniProt: the Universal Protein knowledgebase

  2004cited by this paper
• The Aquila Digital Community The Aquila Digital Community

  year unknowncited by this paper

• Evolutionary profile enhancement improves protein function annotation for remote homologs

  2026influential citation
• Prediction and analysis of new HisKA-like domains

  2026cites this paper
• Investigating Enzyme Function by Geometric Matching of Catalytic Motifs

  2026cites this paper
• Structural and functional annotation of Glaciozyma antarctica hypothetical proteins using integrated modeling pipelines

  2025cites this paper
• Chromosome-level genome assembly of the traditional Chinese medical plant Pseudostellaria heterophylla

  2025cites this paper
• A chromosomal-level genome assembly of Aulacophora lewisii Baly, 1886 (Coleoptera: Chrysomelidae)

  2025cites this paper
• An Asgard archaeon with internal membrane compartments

  2025influential citation
• Generative Artificial Intelligence in Bioinformatics: A Systematic Review of Models, Applications, and Methodological Advances

  2025cites this paper
• Genomic signatures associated with convergent funnel-web building behavior in spiders

  2025cites this paper
• A chromosomal-level genome assembly of Omiodes indicata Fabricius (Lepidoptera: Crambidae)

  2025cites this paper
• NAC controls nascent chain fate through tunnel sensing and chaperone action

  2025cites this paper
• Chromosome-level genome of the shining chafers Kibakoganea tamdaoensis (Coleoptera: Scarabaeidae: Rutelinae)

  2025cites this paper
• Prediction of Intrinsic Disorder Functions with DEPICTER2.

  2025cites this paper
• A High-Quality Chromosome-Level Genome Assembly and Comparative Analyses Provide Insights into the Adaptation of Chrysomya megacephala (Fabricius, 1794) (Diptera: Calliphoridae)

  2025influential citation
• A chromosomal-level genome assembly of Odontolabis cuvera Hope, 1842 (Coleoptera: Lucanidae)

  2025cites this paper
• Phosphoproteomic insights into the regulation of root length in rice (Oryza sativa L. cv. KDML 105): uncovering key events and pathways involving phosphorylated proteins

  2025cites this paper
• A hybrid de novo genome assembly of the digger wasp Cerceris sabulosa (Hymenoptera, Crabronidae).

  2025cites this paper
• A chromosomal-level genome assembly of Kibakoganea sinica, Bouchard, 2005 (Coleoptera: Scarabaeidae)

  2025cites this paper
• Chromosome-level genome assembly of Sambus kanssuensis (Coleoptera: Buprestidae)

  2025cites this paper
• A chromosomal-level genome assembly of Araneus marmoreus Schenkel, 1953 (Araneae: Araneidae)

  2025cites this paper
• Chromosome-level genome assembly of Parotis chlorochroalis (Lepidoptera: Crambidae: Spilomelinae)

  2025cites this paper
• Haplotype-resolved reference genomes of the sea turtle clade unveil ultra-syntenic genomes with hotspots of divergence

  2025cites this paper
• An Overview and Comparative Analysis of CRISPR-SpCas9 gRNA Activity Prediction Tools

  2025cites this paper
• High-quality genome assembly of the azooxanthellate coral Tubastraea coccinea (Lesson, 1829)

  2025cites this paper
• Comprehensive genome annotation of Bombyx mori p50ma strain, a newly developed standard strain

  2025cites this paper
• Learning maximally spanning representations improves protein function annotation

  2025cites this paper
• Crystal structure of dihydroorotate dehydrogenase from Helicobacter pylori with bound flavin mononucleotide.

  2025cites this paper
• A chromosome-level genome assembly of Mylabris sibirica Fischer von Waldheim, 1823 (Coleoptera, Meloidae)

  2025cites this paper
• De novo genome hybrid assembly and annotation of the endangered and euryhaline fish Aphanius iberus (Valenciennes, 1846) with identification of genes potentially involved in salinity adaptation

  2025cites this paper
• SEGT-GO: a graph transformer method based on PPI serialization and explanatory artificial intelligence for protein function prediction

  2025cites this paper
• A chromosome-level genome assembly of wild silkmoth, Bombyx mandarina

  2025influential citation
• Comprehensive genome annotation of Trilocha varians, a new model species of Lepidopteran insects

  2025influential citation
• Near T2T haplotype-resolved genomes of cacao (Theobroma cacao) variety CCN51

  2025cites this paper
• NAC controls nascent chain fate through tunnel sensing and chaperone action.

  2025cites this paper
• A chromosome-level genome assembly of Prosopocoilus inquinatus Westwood, 1848 (Coleoptera: Lucanidae)

  2024cites this paper
• A chromosome-level genome assembly of Serangium japonicum Chapin, 1940 (Coleoptera: Coccinellidae)

  2024cites this paper
• Viro3D: a comprehensive database of virus protein structure predictions

  2024influential citation
• Rational engineering of allosteric protein switches by in silico prediction of domain insertion sites

  2024cites this paper
• CATH v4.4: major expansion of CATH by experimental and predicted structural data

  2024cites this paper
• Clustering protein functional families at large scale with hierarchical approaches

  2024cites this paper
• Newly Developed Structure-Based Methods Do Not Outperform Standard Sequence-Based Methods for Large-Scale Phylogenomics

  2024cites this paper
• The chromosome-level genome assembly of Aphidoletes aphidimyza Rondani (Diptera: Cecidomyiidae)

  2024cites this paper
• Deep learning methods for protein function prediction

  2024cites this paper
• Structure-based protein and small molecule generation using EGNN and diffusion models: A comprehensive review

  2024cites this paper
• Single-molecule imaging reveals the mechanism of bidirectional replication initiation in metazoa.

  2024cites this paper
• Chromosome-level genome assembly of the snakefly Mongoloraphidia duomilia (Raphidioptera: Raphidiidae)

  2024cites this paper
• Exploring structural diversity across the protein universe with The Encyclopedia of Domains

  2024cites this paper
• Machine learning-based prediction of proteins’ architecture using sequences of amino acids and structural alphabets

  2024cites this paper
• Genomic insights into the chromosomal elongation in a family of Collembola

  2024influential citation
• Chromosome-scale genome assemblies of Himalopsyche anomala and Eubasilissa splendida (Insecta: Trichoptera)

  2024cites this paper
• Genome assembly of Medicago truncatula accession SA27063 provides insight into spring black stem and leaf spot disease resistance

  2024influential citation
• Single-cell analysis of isoform switching and transposable element expression during preimplantation embryonic development

  2024cites this paper
• The C‐terminus is essential for the stability of the mycobacterial channel protein MspA

  2024cites this paper
• N-glycosylation as a eukaryotic protective mechanism against protein aggregation

  2024cites this paper
• Predictive Modeling of Proteins Encoded by a Plant Virus Sheds a New Light on Their Structure and Inherent Multifunctionality

  2024cites this paper
• A chromosomal-level genome assembly of Corcyra cephalonica Stainton (Lepidoptera: Pyralidae)

  2024cites this paper
• Unsupervised domain classification of AlphaFold2-predicted protein structures

  2024cites this paper
• A chromosomal-level genome assembly of Serrognathus titanus Boisduval, 1835 (Coleoptera: Lucanidae)

  2024cites this paper
• Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus

  2023cites this paper
• Structural coverage of the human interactome

  2023cites this paper
• Lampshade web spider Ectatosticta davidi chromosome-level genome assembly provides evidence for its phylogenetic position

  2023cites this paper
• The genome of sheep ked (Melophagus ovinus) reveals potential mechanisms underlying reproduction and narrower ecological niches

  2023influential citation
• The genome of the glasshouse plant noble rhubarb (Rheum nobile) provides a window into alpine adaptation

  2023cites this paper
• Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study

  2023cites this paper
• CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins

  2023cites this paper
• The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors.

  2023cites this paper
• Exploring structural features and potential lipid interactions of Pseudomonas aeruginosa type three secretion effector PemB by spectroscopic and calorimetric experiments

  2023cites this paper
• Advances in machine intelligence‐driven virtual screening approaches for big‐data

  2023cites this paper
• Learning sequence, structure, and function representations of proteins with language models

  2023cites this paper
• Tutorial: a guide for the selection of fast and accurate computational tools for the prediction of intrinsic disorder in proteins

  2023cites this paper
• Protein remote homology detection and structural alignment using deep learning

  2023cites this paper
• The first chromosome-level genome assembly of Entomobrya proxima Folsom, 1924 (Collembola: Entomobryidae)

  2023cites this paper
• N-glycosylation as a eukaryotic protective mechanism against protein aggregation

  2023influential citation
• Chromosome-Scale Genome Assembly of the Solitary Parasitoid Wasp Microplitis manilae Ashmead, 1904 (Braconidae: Microgastrinae)

  2023cites this paper
• A chromosome-level genome assembly and intestinal transcriptome of Trypoxylus dichotomus (Coleoptera: Scarabaeidae) to understand its lignocellulose digestion ability

  2022cites this paper
• Exploring Manually Curated Annotations of Intrinsically Disordered Proteins with DisProt

  2022cites this paper
• Population genomics provides insights into lineage divergence and local adaptation within the cotton bollworm

  2022cites this paper
• A simple guide to de novo transcriptome assembly and annotation

  2022cites this paper
• Ultrafast end-to-end protein structure prediction enables high-throughput exploration of uncharacterized proteins

  2022cites this paper
• A Chromosome-Level Genome Assembly of the Parasitic Wasp Chelonus formosanus Sonan 1932 (Hymenoptera: Braconidae)

  2022cites this paper
• Chromosome-Level Genome Assembly of Anthidium xuezhongi Niu & Zhu, 2020 (Hymenoptera: Apoidea: Megachilidae: Anthidiini)

  2022cites this paper
• CATHe: detection of remote homologues for CATH superfamilies using embeddings from protein language models

  2022cites this paper
• Chromosomal-Level Genome Assembly of the Springtail Tomocerus qinae (Collembola: Tomoceridae)

  2022cites this paper
• Resources for computational prediction of intrinsic disorder in proteins.

  2022influential citation
• A De Novo Chromosome-Level Genome Assembly of the White-Tailed Deer, Odocoileus Virginianus

  2022cites this paper
• Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models

  2022cites this paper
• AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms

  2022cites this paper
• AlkB RNA demethylase homologues and N 6 ‐methyladenosine are involved in Potyvirus infection

  2022cites this paper
• Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus

  2022cites this paper
• ProGen2: Exploring the Boundaries of Protein Language Models

  2022influential citation
• Accounting for small variations in the tracrRNA sequence improves sgRNA activity predictions for CRISPR screening

  2022cites this paper
• Dissecting peripheral protein-membrane interfaces

  2022cites this paper
• A Long-Read Genome Assembly of a Native Mite in China Pyemotes zhonghuajia Yu, Zhang & He (Prostigmata: Pyemotidae) Reveals Gene Expansion in Toxin-Related Gene Families

  2022cites this paper
• Climate-Endangered Arctic Epishelf Lake Harbors Viral Assemblages with Distinct Genetic Repertoires

  2022cites this paper
• The genome of homosporous maidenhair fern sheds light on the euphyllophyte evolution and defences

  2022cites this paper
• The First Chromosome-level Genome Assembly of Cheumatopsyche charites Malicky and Chantaramongkol, 1997 (Trichoptera: Hydropsychidae) Reveals How It Responds to Pollution

  2022cites this paper
• Functional Analysis of Hypothetical Proteins of Vibrio parahaemolyticus Reveals the Presence of Virulence Factors and Growth-Related Enzymes With Therapeutic Potential

  2022cites this paper
• Comparison of functional classification systems

  2022cites this paper
• Protein sequence design with a learned potential

  2022influential citation
• A chromosome‐level genome of the spider Trichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event

  2021influential citation