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Paysan-Lafosse T, Blum M, Chuguransky S, Grego T, Pinto BL, Salazar G, Bileschi M, Bork P, Bridge A, Colwell L, Gough J, Haft D, Letunić I, Marchler-Bauer A, Mi H, Natale D, Orengo C, Pandurangan A, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu C, Bateman A. InterPro in 2022. Nucleic Acids Res 2023; 51:D418-D427. [PMID: 36350672 PMCID: PMC9825450 DOI: 10.1093/nar/gkac993] [Citation(s) in RCA: 483] [Impact Index Per Article: 483.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/12/2022] [Accepted: 10/28/2022] [Indexed: 11/11/2022] Open
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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Affiliation(s)
- Typhaine Paysan-Lafosse
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Matthias Blum
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Sara Chuguransky
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Tiago Grego
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Beatriz Lázaro Pinto
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Gustavo A Salazar
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | | | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
- Yonsei Frontier Lab (YFL), Yonsei University, 03722 Seoul, South Korea
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Alan Bridge
- Swiss-Prot Group, Swiss Institute of Bioinformatics, CMU, 1 rue Michel Servet, CH-1211, Geneva 4, Switzerland
| | - Lucy Colwell
- Google Research, Brain team, Cambridge, MA, USA
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Julian Gough
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Ave, Trumpington, Cambridge CB2 0QH, UK
| | - Daniel H Haft
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Ivica Letunić
- Biobyte Solutions GmbH, Bothestr 142, 69126 Heidelberg, Germany
| | - Aron Marchler-Bauer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Huaiyu Mi
- Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Darren A Natale
- Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Christine A Orengo
- Department of Structural and Molecular Biology, University College London, Gower St, Bloomsbury, London WC1E 6BT, UK
| | - Arun P Pandurangan
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Ave, Trumpington, Cambridge CB2 0QH, UK
- Department of Biochemistry, Sanger Building, University of Cambridge, Cambridge, UK
| | - Catherine Rivoire
- Swiss-Prot Group, Swiss Institute of Bioinformatics, CMU, 1 rue Michel Servet, CH-1211, Geneva 4, Switzerland
| | - Christian J A Sigrist
- Swiss-Prot Group, Swiss Institute of Bioinformatics, CMU, 1 rue Michel Servet, CH-1211, Geneva 4, Switzerland
| | - Ian Sillitoe
- Department of Structural and Molecular Biology, University College London, Gower St, Bloomsbury, London WC1E 6BT, UK
| | - Narmada Thanki
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Paul D Thomas
- Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padua, via U. Bassi 58/b, 35131 Padua, Italy
| | - Cathy H Wu
- Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA
- Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
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