CATH: comprehensive structural and functional annotations for genome sequences

By Ian Sillitoe, Tony E. Lewis, Alison L. Cuff, Sayoni Das, P. Ashford, N. Dawson, Nicholas Furnham, Roman A. Laskowski, David A. Lee, Jonathan G. Lees and 4 more. 2014

439 citations recorded by the source corpus.

The latest version of the CATH-Gene3D protein structure classification database (4.0, http://www.cathdb.info) provides annotations for over 235 000 protein domain structures and includes 25 million domain predictions. This article provides an update on the major developments in the 2 years since the last publication in this journal including: significant improvements to the predictive power of our functional families (FunFams); the release of our ‘current’ putative domain assignments (CATH-B); a new, strictly non-redundant data set of CATH domains suitable for homology benchmarking experiments (CATH-40) and a number of improvements to the web pages.

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Citations in the corpus

The SWISS-MODEL Repository—new features and functionality (2016, background): “The computational structural biology community has a long tradition of providing protein model databases such as the Genomic Threading Database (4,5), ModBase (6), Genome 3D (7), GPCRdb (8) and SWISS-MODEL Repository (SMR) (9) as well as protein functional annotation databases such as Superfamily (1”
CATH: an expanded resource to predict protein function through structure and sequence (2016, background): “This list of domain definitions and superfamily assignments is updated daily (1) and is available to download in a number of different formats.”
InterPro in 2017—beyond protein family and domain annotations (2016, background): “InterPro entries are also automatically annotated with cross-references to a range of relevant databases, including the pathway databases ENZYME (18), MetaCyc (19), UniPathway (20) and KEGG (21), and various 3D structure databases (22,23).”
Sixty-five years of the long march in protein secondary structure prediction: the final stretch? (2016, background): “Proteins can perform a wide variety of molecular functions [1] ranging from molecular recognition, catalysis, molecular motors, to structural support, in part because they can fold into many different threedimensional structural shapes [2, 3].”
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces (2017, unknown): “CATH domains (28) are depicted in colors specific to their first and second level classification.”
HMMER web server: 2015 update (2015, methodology): “Furthermore, the HMMER3 based protein family databases CATH-Gene3D (20), PIRSF (21), Superfamily (22) and TIGRFAMs (23) have been incorporated into the hmmscan search as alternative target HMM databases.”
BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra (2018, background): “2 (16) and the corresponding secondary structure compositions calculated from the respecting PDB structures.”
GOLabeler: Improving Sequence-based Large-scale Protein Function Prediction by Learning to Rank (2017, methodology): “InterPro [21] combines 14 diﬀerent protein and domain family databases, including Pfam [28], CATH-Gene3D [27], CCD [20] and SUPER-FAMILY [8], so covering a large number of protein families, domains and motifs in sequences.”
PDBsum: Structural summaries of PDB entries (2017, methodology): “The Swiss-3Dimage collection 4 and the IMB Jena Image Library of Biological Macromolecules 5 focused on beautiful images of protein structures, while other databases specialized in particular aspects of structure—such as the fold classification systems of SCOP 6 and CATH.”
Global organization of a binding site network gives insight into evolution and structure-function relationships of proteins (2017, methodology): “For domain composition Shannon information calculation, the chain IDs of residues participating in forming a binding site were identified and their domain IDs defined by the CATH database 19, 69 were used.”
BRENDA in 2019: a European ELIXIR core data resource (2018, methodology): “The 3D-structural classification of enzyme proteins is covered by SCOPe and CATH (10,11).”
BRENDA, the ELIXIR core data resource in 2021: new developments and updates (2020, background): “CATH and SCOPe cover the 3D structural classification of enzymes (12,13).”