InterPro in 2022

Typhaine Paysan-Lafosse¹, Matthias Blum¹, Sara Chuguransky¹, Tiago Grego¹, Beatriz Lázaro Pinto¹, Gustavo A Salazar¹, Maxwell L Bileschi², Peer Bork^{3

4

5}, Alan Bridge⁶, Lucy Colwell^{2

7}, Julian Gough⁸, Daniel H Haft⁹, Ivica Letunić¹⁰, Aron Marchler-Bauer⁹, Huaiyu Mi¹¹, Darren A Natale¹², Christine A Orengo¹³, Arun P Pandurangan^{8

14}, Catherine Rivoire⁶, Christian J A Sigrist⁶, Ian Sillitoe¹³, Narmada Thanki⁹, Paul D Thomas¹¹, Silvio C E Tosatto¹⁵, Cathy H Wu^{12

16}, Alex Bateman¹

Affiliations

¹ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
² Google Research, Brain team, Cambridge, MA, USA.
³ European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
⁴ Yonsei Frontier Lab (YFL), Yonsei University, 03722 Seoul, South Korea.
⁵ Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany.
⁶ Swiss-Prot Group, Swiss Institute of Bioinformatics, CMU, 1 rue Michel Servet, CH-1211, Geneva 4, Switzerland.
⁷ Department of Chemistry, University of Cambridge, Cambridge, UK.
⁸ Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Ave, Trumpington, Cambridge CB2 0QH, UK.
⁹ National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA.
¹⁰ Biobyte Solutions GmbH, Bothestr 142, 69126 Heidelberg, Germany.
¹¹ Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA.
¹² Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA.
¹³ Department of Structural and Molecular Biology, University College London, Gower St, Bloomsbury, London WC1E 6BT, UK.
¹⁴ Department of Biochemistry, Sanger Building, University of Cambridge, Cambridge, UK.
¹⁵ Department of Biomedical Sciences, University of Padua, via U. Bassi 58/b, 35131 Padua, Italy.
¹⁶ Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA.

PMID: 36350672
PMCID: PMC9825450
DOI: 10.1093/nar/gkac993

InterPro in 2022

Typhaine Paysan-Lafosse et al. Nucleic Acids Res. 2023.

. 2023 Jan 6;51(D1):D418-D427.

doi: 10.1093/nar/gkac993.

Authors

Affiliations

¹ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
² Google Research, Brain team, Cambridge, MA, USA.
³ European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
⁴ Yonsei Frontier Lab (YFL), Yonsei University, 03722 Seoul, South Korea.
⁵ Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany.
⁶ Swiss-Prot Group, Swiss Institute of Bioinformatics, CMU, 1 rue Michel Servet, CH-1211, Geneva 4, Switzerland.
⁷ Department of Chemistry, University of Cambridge, Cambridge, UK.
⁸ Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Ave, Trumpington, Cambridge CB2 0QH, UK.
⁹ National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA.
¹⁰ Biobyte Solutions GmbH, Bothestr 142, 69126 Heidelberg, Germany.
¹¹ Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA.
¹² Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA.
¹³ Department of Structural and Molecular Biology, University College London, Gower St, Bloomsbury, London WC1E 6BT, UK.
¹⁴ Department of Biochemistry, Sanger Building, University of Cambridge, Cambridge, UK.
¹⁵ Department of Biomedical Sciences, University of Padua, via U. Bassi 58/b, 35131 Padua, Italy.
¹⁶ Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA.

PMID: 36350672
PMCID: PMC9825450
DOI: 10.1093/nar/gkac993

Abstract

The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. Here, we report recent developments with InterPro (version 90.0) and its associated software, including updates to data content and to the website. These developments extend and enrich the information provided by InterPro, and provide a more user friendly access to the data. Additionally, we have worked on adding Pfam website features to the InterPro website, as the Pfam website will be retired in late 2022. We also show that InterPro's sequence coverage has kept pace with the growth of UniProtKB. Moreover, we report the development of a card game as a method of engaging the non-scientific community. Finally, we discuss the benefits and challenges brought by the use of artificial intelligence for protein structure prediction.

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Figures

**Figure 1.**
Navigation menus have been updated in multiple places on the InterPro website. The website main menu tabs now expand as dropdowns and breadcrumbs allow to know where pages are located on the website (A), the menu in entry pages is displayed on the left-hand side and can be collapsed (B), the main data type in the browse feature can be chosen from the *Browse* dropdown menu and filters are now displayed on the left-hand side (C).

**Figure 2.**
Protein sequence viewer with the *Residues* section for UniProtKB: P18207.

**Figure 3.**
Taxonomy sunburst view for PF00120.

**Figure 4.**
Domain architectures display changes between InterPro 87.0 (A) and InterPro 88.0 (B) for PF00120.

**Figure 5.**
Protein family game landing page in Tabletopia.

See this image and copyright information in PMC

References

1. Sillitoe I., Bordin N., Dawson N., Waman V.P., Ashford P., Scholes H.M., Pang C.S.M., Woodridge L., Rauer C., Sen N.et al. .. CATH: increased structural coverage of functional space. Nucleic Acids Res. 2021; 49:D266–D273. - PMC - PubMed
1. Lu S., Wang J., Chitsaz F., Derbyshire M.K., Geer R.C., Gonzales N.R., Gwadz M., Hurwitz D.I., Marchler G.H., Song J.S.et al. .. CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Res. 2020; 48:D265–D268. - PMC - PubMed
1. Pedruzzi I., Rivoire C., Auchincloss A.H., Coudert E., Keller G., de Castro E., Baratin D., Cuche B.A., Bougueleret L., Poux S.et al. .. HAMAP in 2015: updates to the protein family classification and annotation system. Nucleic Acids Res. 2015; 43:D1064–D1070. - PMC - PubMed
1. Mi H., Ebert D., Muruganujan A., Mills C., Albou L.-P., Mushayamaha T., Thomas P.D.. PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API. Nucleic Acids Res. 2021; 49:D394–D403. - PMC - PubMed
1. Mistry J., Chuguransky S., Williams L., Qureshi M., Salazar G.A., Sonnhammer E.L.L., Tosatto S.C.E., Paladin L., Raj S., Richardson L.J.et al. .. Pfam: the protein families database in 2021. Nucleic Acids Res. 2021; 49:D412–D419. - PMC - PubMed

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InterPro in 2022

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InterPro in 2022

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