ArticleNucleic acids research2008
Gene3D: comprehensive structural and functional annotation of genomes.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 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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Who cites it
35 citing papers in PubMed.
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- Chromosome-level genome assembly of Cryptosporidium parvum by long-read sequencing of ten oocysts.Scientific data · 2024Article
- Prokaryotic and Highly-Repetitive WD40 Proteins: A Systematic Study.Scientific reports · 2017Article
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- An assessment of the amount of untapped fold level novelty in under-sampled areas of the tree of life.Scientific reports · 2015Article
- The enzymatic nature of an anonymous protein sequence cannot reliably be inferred from superfamily level structural information alone.Protein science : a publication of the Protein Society · 2015Article
- BambooGDB: a bamboo genome database with functional annotation and an analysis platform.Database : the journal of biological databases and curation · 2014Article
- New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.Nucleic acids research · 2013Article
- Uncovering the molecular machinery of the human spindle--an integration of wet and dry systems biology.PloS one · 2012Article
- Internal organization of large protein families: relationship between the sequence, structure, and function-based clustering.Proteins · 2011Article
- Immunogenicity of autoantigens.BMC genomics · 2011Article
- The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods.Journal of structural and functional genomics · 2011Article
- Extending CATH: increasing coverage of the protein structure universe and linking structure with function.Nucleic acids research · 2011Article
- Detailed analysis of function divergence in a large and diverse domain superfamily: toward a refined protocol of function classification.Structure (London, England : 1993) · 2010Article
- Protein annotation and modelling servers at University College London.Nucleic acids research · 2010Article
- CODA: accurate detection of functional associations between proteins in eukaryotic genomes using domain fusion.PloS one · 2010Article
- From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase.Cellular and molecular life sciences : CMLS · 2010Review
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene3D provides comprehensive structural and functional annotation of most available protein sequences, including the UniProt, RefSeq and Integr8 resources. The main structural annotation is generated through scanning these sequences against the CATH structural domain database profile-HMM library. CATH is a database of manually derived PDB-based structural domains, placed within a hierarchy reflecting topology, homology and conservation and is able to infer more ancient and divergent homology relationships than sequence-based approaches. This data is supplemented with Pfam-A, other non-domain structural predictions (i.e. coiled coils) and experimental data from UniProt. In order to enhance the investigations possible with this data, we have also incorporated a variety of protein annotation resources, including protein-protein interaction data, GO functional assignments, KEGG pathways, FUNCAT functional descriptions and links to microarray expression data. All of this data can be accessed through a newly re-designed website that has a focus on flexibility and clarity, with searches that can be restricted to a single genome or across the entire sequence database. Currently Gene3D contains over 3.5 million domain assignments for nearly 5 million proteins including 527 completed genomes. This is available at: http://gene3d.biochem.ucl.ac.uk/
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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.