Waman, Vaishali P;
Bordin, Nicola;
Lau, Andy;
Kandathil, Shaun;
Wells, Jude;
Miller, David;
Velankar, Sameer;
... Orengo, Christine; + view all
(2024)
CATH v4.4: major expansion of CATH by experimental and predicted structural data.
Nucleic Acids Research
, Article gkae1087. 10.1093/nar/gkae1087.
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Abstract
CATH (https://www.cathdb.info) is a structural classification database that assigns domains to the structures in the Protein Data Bank (PDB) and AlphaFold Protein Structure Database (AFDB) and adds layers of biological information, including homology and functional annotation. This article covers developments in the CATH classification since 2021. We report the significant expansion of structural information (180-fold) for CATH superfamilies through classification of PDB domains and predicted domain structures from the Encyclopedia of Domains (TED) resource. TED provides information on predicted domains in AFDB. CATH v4.4 represents an expansion of ∼64 844 experimentally determined domain structures from PDB. We also present a mapping of ∼90 million predicted domains from TED to CATH superfamilies. New PDB and TED data increases the number of superfamilies from 5841 to 6573, folds from 1349 to 2078 and architectures from 41 to 77. TED data comprises predicted structures, so these new folds and architectures remain hypothetical until experimentally confirmed. CATH also classifies domains into functional families (FunFams) within a superfamily. We have updated sequences in FunFams by scanning FunFam-HMMs against UniProt release 2024_02, giving a 276% increase in FunFams coverage. The mapping of TED structural domains has resulted in a 4-fold increase in FunFams with structural information.
| Type: | Article |
|---|---|
| Title: | CATH v4.4: major expansion of CATH by experimental and predicted structural data |
| Location: | England |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1093/nar/gkae1087 |
| Publisher version: | https://doi.org/10.1093/nar/gkae1087 |
| Language: | English |
| Additional information: | © The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > UCL BEAMS UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Computer Science UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Structural and Molecular Biology |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10200738 |
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