The InterPro protein families and domains database: 20 years on

By Matthias Blum, Hsin-Yu Chang, S. Chuguransky, Tiago Grego, Swaathi Kandasamy, Alex L. Mitchell, Gift Nuka, T. Paysan-Lafosse, Matloob Qureshi, Shriya Raj and 23 more. Nucleic Acids Res., 2020

1,852 citations recorded by the source corpus.

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. InterProScan is the underlying software that allows protein and nucleic acid sequences to be searched against InterPro's signatures. Signatures are predictive models which describe protein families, domains or sites, and are provided by multiple databases. InterPro combines signatures representing equivalent families, domains or sites, and provides additional information such as descriptions, literature references and Gene Ontology (GO) terms, to produce a comprehensive resource for protein classification. Founded in 1999, InterPro has become one of the most widely used resources for protein family annotation. Here, we report the status of InterPro (version 81.0) in its 20th year of operation, and its associated software, including updates to database content, the release of a new website and REST API, and performance improvements in InterProScan.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/317325439a0ce543d7629848a35adea04b6e7d12

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In Materials Chemistry

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4. Paul D. Thomas
5. Huaiyu Mi
6. S. Velankar
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In Molecular Biology

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5. Gerard J. Kleywegt

Citations in the corpus

• Coevolution‐derived native and non‐native contacts determine the emergence of a novel fold in a universally conserved family of transcription factors (2022, methodology): “All initial RfaH sequences were retrieved from the Interpro database of protein families.(24) The choice of this database for sequence retrieval is due to a recent study that employed this database to characterize the sequence conservation in both RfaH and NusG and further experimentally tested subs”
• Search and sequence analysis tools services from EMBL-EBI in 2022 (2022, neutral): “…as NCBI BLAST+ (8) and FASTA (9), multiple sequence alignment and pairwise sequence alignment tools, such as Clustal Omega (10) and Kalign (11), tools for functional annotation and prediction such as InterProScan 5 (12), RNA analysis tools such as R2DT (13), to other sequence analysis utilities.”
• Transcription factors interact with RNA to regulate genes (2022, methodology): “For the adjacency analysis, DNA-binding domains were defined based on domains with annotations of DNA-binding in Interpro (Blum et al., 2021).”
• InterPro in 2022 (2022, neutral): “3% of sequences in the UniProt Archive (UniParc) were annotated by InterPro (20).”
• FlyBase: a guided tour of highlighted features (2022, methodology): “Protein Domains Searches for genes whose products contain a specific protein domain, repeat, or site using InterPro identifiers or signatures (Blum et al. 2021).”
• RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning (2022, neutral): “InterPro (83) Classification of Protein Families”
• DALI shines a light on remote homologs: One hundred discoveries (2022, positive): “And if these were uninformative, we would additionally check: (i) Pannzer predictions (Törönen et al., 2018); (ii) the crystallographic literature at the RCSB site (https://www.rcsb.org/; Berman et al., 2000) or (iii) crosslinks to InterPro (Blum et al., 2021) in the UniProt entry via Pannzer/SANS l”
• PANTHER: Making genome‐scale phylogenetics accessible to all (2021, methodology): “20 PAN-THER HMMs (and soon also trees) are imported into the InterPro resource, where they are used for classification of UniProt proteins, and redistributed in the widely-used InterProScan software package 43 for large-scale protein annotation.”
• OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity (2022, methodology): “As the main source of the genomes for the release is RefSeq/GenBank, the protein sequence annotation available from NCBI is supplemented by mapped identifiers and textual descriptions from Uniprot (59%) (17), Ensembl/ENA (60%) (18), NCBI gid (34%), InterPro (49%) (19) and GO (42% total: 27% molecula”
• AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models (2021, methodology): “UniProt (5), Pfam (18), InterPro (19) and PDBeKB (7) use this API to display AlphaFold models on their web pages.”