Abstract
Gene3D (http://gene3d.biochem.ucl.ac.uk) is a database of protein domain structure annotations for protein sequences. Domains are predicted using a library of profile HMMs from 2738 CATH superfamilies. Gene3D assigns domain annotations to Ensembl and UniProt sequence sets including >6000 cellular genomes and >20 million unique protein sequences. This represents an increase of 45% in the number of protein sequences since our last publication. Thanks to improvements in the underlying data and pipeline, we see large increases in the domain coverage of sequences. We have expanded this coverage by integrating Pfam and SUPERFAMILY domain annotations, and we now resolve domain overlaps to provide highly comprehensive composite multi-domain architectures. To make these data more accessible for comparative genome analyses, we have developed novel search algorithms for searching genomes to identify related multi-domain architectures. In addition to providing domain family annotations, we have now developed a pipeline for 3D homology modelling of domains in Gene3D. This has been applied to the human genome and will be rolled out to other major organisms over the next year.
Highlights
Proteins commonly contain !1 discrete independently folding domains
In addition to providing domain family annotations, we have developed a pipeline for 3D homology modelling of domains in Gene3D
After the domains have been assigned to a protein, DomainFinder [5] is used to resolve issues of overlapping domain assignments to derive a single combination of domains known as the multi-domain architecture (MDA)
Summary
Proteins commonly contain !1 discrete independently folding domains. Similar to these folded domains, it is becoming increasingly clear that many proteins can contain long disordered sections that are of functional importance. Gene3D assigns domain annotations to Ensembl and UniProt sequence sets including >6000 cellular genomes and >20 million unique protein sequences. In addition to providing domain family annotations, we have developed a pipeline for 3D homology modelling of domains in Gene3D.
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