Extending CATH: increasing coverage of the protein structure universe and linking structure with function

Abstract

CATH version 3.3 (class, architecture, topology, homology) contains 128 688 domains, 2386 homologous superfamilies and 1233 fold groups, and reflects a major focus on classifying structural genomics (SG) structures and transmembrane proteins, both of which are likely to add structural novelty to the database and therefore increase the coverage of protein fold space within CATH. For CATH version 3.4 we have significantly improved the presentation of sequence information and associated functional information for CATH superfamilies. The CATH superfamily pages now reflect both the functional and structural diversity within the superfamily and include structural alignments of close and distant relatives within the superfamily, annotated with functional information and details of conserved residues. A significantly more efficient search function for CATH has been established by implementing the search server Solr (http://lucene.apache.org/solr/). The CATH v3.4 webpages have been built using the Catalyst web framework.

The Protein Data Bank archive as an open data resource

“…More than 400 million coordinate sets were downloaded in 2013 from the wwPDB partner sites. Both the utility and the uniformity of PDB data have enabled the development of other databases and datarelated resources, including resources for drug discovery (for a review see [32]); resources focused on small molecules and ligands such as ChEMBL [33], DrugBank [34], BindingDB [35], BindingMOAD [36], and PDBBind [37]; protein structure classification and annotation resources, such as CATH [38,39], SCOP [40][41][42], and PDBsum [43,44]; and focused, specialty annotation resources such as Protein Data Bank of Transmembrane Proteins (PDBTM) [45], ArchDB for functional loops in structures [46], and 3did for protein-protein interaction surfaces [47]. These resources are frequently compiled in the annual Database Issue of Nucleic Acids Research.…”

In vivo translation rates can substantially delay the cotranslational folding of the Escherichia coli cytosolic proteome

“…Full details of the construction of this database are provided in Supplemental Information. Briefly, for the 4,319 unique coding sequences in the E. coli transcriptome, we identified those that had an X-ray structure in the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB) (14) with a resolution of less than or equal to 3 Å or an NMR entry, and also had domain definitions in the Structural Classification of Proteins (SCOP) (15) or CATH (16) database. This procedure resulted in 802 proteins.…”

Structure-to-Function Computational Prediction of a Subset of Ribosomal Proteins for the Small Ribosome Subunit

“…To search for structural neighbours, constructed 3D models of the RPs were submitted as Protein Data Bank (PDB) file to the Vector Alignment Search Tool (VAST) server (http://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html). The algorithm of the analysis involves a search against medium-redundancy subset of PDB, and the structural alignment of the query protein with its corresponding structure neighbours [13] [16], [17]) were employed for functional annotation of the RPs in order to computationally derive logical functions.…”