Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis

By Jonathan G. Lees, C. Yeats, J. Perkins, Ian Sillitoe, R. Rentzsch, Benoit H. Dessailly, Christine A. Orengo. 2011

114 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

Learning inverse folding from millions of predicted structures (2022, methodology): “We created a filtered version of UniRef100 by searching all the validation-split and test-split Gene3D HMMs against UniRef100 (202001) and excluding all hits.”
Protein structure prediction from sequence variation (2012, background): “However, this shortcoming may be addressed simply over time, and more sophisticated use of family and subfamily information 54 may improve the accuracy of the algorithms.”
Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models (2014, methodology): “They are, for example, used in the annotation of both protein domains [6-9] and genomic sequence derived from ancient transposable element expansions [10].”
InterProScan 5: genome-scale protein function classification (2014, methodology): “By default, InterProScan 5 uses a pure in-memory database, which requires no configuration.”
MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins (2017, methodology): “Gene3D (38) contributes complementary order annotation to the MobiDB consensus calculation, while Pfam (39) is used to highlight protein domains.”
Protein Modelling: What Happened to the “Protein Structure Gap”? (2013, unknown): “Modeling protein complexes and interactions Although structural protein domains often reflect functional modules (Lees et al., 2012), they are rarely found in isolation: many proteins form intricate multi-domain architectures, often assemble to stable oligomeric quaternary states, and frequently…”