Lau, Andy M;
Bordin, Nicola;
Kandathil, Shaun M;
Sillitoe, Ian;
Waman, Vaishali P;
Wells, Jude;
Orengo, Christine A;
(2024)
Exploring structural diversity across the protein universe with The Encyclopedia of Domains.
Science
, 386
(6721)
, Article eadq4946. 10.1126/science.adq4946.
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Abstract
The AlphaFold Protein Structure Database (AFDB) contains more than 214 million predicted protein structures composed of domains, which are independently folding units found in multiple structural and functional contexts. Identifying domains can enable many functional and evolutionary analyses but has remained challenging because of the sheer scale of the data. Using deep learning methods, we have detected and classified every domain in the AFDB, producing The Encyclopedia of Domains. We detected nearly 365 million domains, over 100 million more than can be found by sequence methods, covering more than 1 million taxa. Reassuringly, 77% of the nonredundant domains are similar to known superfamilies, greatly expanding representation of their domain space. We uncovered more than 10,000 new structural interactions between superfamilies and thousands of new folds across the fold space continuum.
| Type: | Article |
|---|---|
| Title: | Exploring structural diversity across the protein universe with The Encyclopedia of Domains |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1126/science.adq4946 |
| Publisher version: | https://doi.org/10.1126/science.adq4946 |
| Language: | English |
| Additional information: | This version is the author accepted manuscript. For information on re-use, please refer to the publisher's terms and conditions. |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > UCL BEAMS UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Computer Science |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10198063 |
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