InterPro in 2019: improving coverage, classification and access to protein sequence annotations

By Alex L. Mitchell, T. Attwood, Patricia C. Babbitt, Matthias Blum, Peer Bork, A. Bridge, Shoshana D. Brown, Hsin-Yu Chang, Sara El-Gebali, M. Fraser and 32 more. 2018

1,309 citations recorded by the source corpus.

Abstract The InterPro database (http://www.ebi.ac.uk/interpro/) classifies protein sequences into families and predicts the presence of functionally important domains and sites. Here, we report recent developments with InterPro (version 70.0) and its associated software, including an 18% growth in the size of the database in terms on new InterPro entries, updates to content, the inclusion of an additional entry type, refined modelling of discontinuous domains, and the development of a new programmatic interface and website. These developments extend and enrich the information provided by InterPro, and provide greater flexibility in terms of data access. We also show that InterPro's sequence coverage has kept pace with the growth of UniProtKB, and discuss how our evaluation of residue coverage may help guide future curation activities.

Subfields: Molecular Biology, Spectroscopy

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Citations in the corpus

HH-suite3 for fast remote homology detection and deep protein annotation (2019, methodology): “Additional computation costs would be marginal, since the version of HHblits presented in this work runs 20 times faster than HMMER, the standard tool for Pfam [20] and InterPro [21] annotations.”
MGnify: the microbiome analysis resource in 2020 (2019, methodology): “In addition, InterPro annotations are processed to generate a compendium of Genome Properties results, detailing whether a property is present, partially present or absent in the dataset. antiSMASH (45) is also run on the predicted protein set, providing annotation of biosynthetic gene clusters.”
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center (2021, neutral): “uk/interpro/) (11), MitoProt (12), STRING (https://string-db.”
The EMBL-EBI search and sequence analysis tools APIs in 2019 (2019, background): “Good examples of such applications are sequence similarity search suites such as NCBI BLAST+ (2), FASTA (3), HMMER3 (4), as well as functional classification and annotation programs such as InterProScan5 (5), which allow large collections of sequence data to be searched.”
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API (2020, methodology): “PANTHER also collaborates with UniProt (15), InterPro (16), and Phylogenes (http://www. phylogenes.org/).”
CDD/SPARCLE: the conserved domain database in 2020 (2019, background): “CDD shares domain models with the InterPro at the European Bioinformatics Institute to supplement sequence annotation with data that are uniquely provided by the CDD curation effort, including protein domain models for very specific subfamilies and the annotation of functional sites.”
Pfam: The protein families database in 2021 (2020, background): “Many functions are also identified by the InterPro database (12) update process which checks whether the UniProtKB / Swiss-Prot descriptions of proteins in each InterPro entry have changed between re-leases.”
PDBe: improved findability of macromolecular structure data in the PDB (2019, neutral): “The ProtVista component (47), developed in collaboration with UniProt and InterPro, enables a graphical visualization of molecular features corresponding to a protein’s primary sequence.”
BRENDA, the ELIXIR core data resource in 2021: new developments and updates (2020, methodology): “KEGG, PATRIC, BrEPS, the best BLAST hit, BKMSreact, InterPro (34) and MMTB.”
The InterPro protein families and domains database: 20 years on (2020, background): “We announced the new InterPro website in the previous NAR paper (20) as a beta release; we have now released it as the main InterPro website.”
UniProt: the universal protein knowledgebase in 2021 (2020, methodology): “In UniProtKB / TrEMBL entries, domains predicted by the InterPro member databases PROSITE, SMART or Pfam are used to automatically provide domain annotations.”
Structure-based protein function prediction using graph convolutional networks (2021, methodology): “We evaluate the function prediction performance by two measures commonly used in the CAFA challenges27 (see “Methods”): (1) protein-centric maximum F-score (Fmax) which measures the accuracy of assigning GO terms/EC numbers to a protein, and is computed as a harmonic mean of the precision and recall”
The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets (2020, background): “The commonly available frameworks are: Gene Ontology annotations (all three GO domains) (45), KEGG pathways (41), UniProt keywords (48), Reactome pathways (42), Pfam (49) and SMART (50) protein domains and In-terPro protein features (51).”