Gene3D: expanding the utility of domain assignments

By S. Lam, N. Dawson, Sayoni Das, Ian Sillitoe, P. Ashford, David A. Lee, Sonja Lehtinen, Christine A. Orengo, Jonathan G. Lees. 2015

68 citations recorded by the source corpus.

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.

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

1. Robin Pearce
2. Yang Zhang
3. Chengxin Zhang
4. Eric W. Bell
5. Yang Li
6. Wei Zheng
7. Xiaogen Zhou
8. Guijun Zhang

Citations in the corpus

• OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more (2020, neutral): “We import genomic and functional data from various different sources, notably Ensembl (10), UniProt (11), RefSeq (12), Gene3D (13) and HGNC/VGNC (14).”
• CATH: an expanded resource to predict protein function through structure and sequence (2016, background): “Additional protein domain sequences with no known structure are identified from UniProtKB (3) and Ensembl (4) protein sequences and classified within our sister resource Gene3D (5).”
• The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces (2017, unknown): “OMA now integrates domain annotations from Gene3D for individual protein entries (27).”
• Gene3D: Extensive prediction of globular domains in proteins (2017, methodology): “There are several important improvements in the current release of Gene3D v16 compared to the v14 published previously (3).”
• I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction (2022, methodology): “The total sequence length of the protein is 152, and the complete domain de fi nition should be ‘ 1 – 51;52 – 105;106 – 152; ’ as de fi ned in the CATH database.”