Dataset Information

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

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.

SUBMITTER: Mitchell AL

PROVIDER: S-EPMC6323941 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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

Mitchell Alex L AL Attwood Teresa K TK Babbitt Patricia C PC Blum Matthias M Bork Peer P Bridge Alan A Brown Shoshana D SD Chang Hsin-Yu HY El-Gebali Sara S Fraser Matthew I MI Gough Julian J Haft David R DR Huang Hongzhan H Letunic Ivica I Lopez Rodrigo R Luciani Aurélien A Madeira Fabio F Marchler-Bauer Aron A Mi Huaiyu H Natale Darren A DA Necci Marco M Nuka Gift G Orengo Christine C Pandurangan Arun P AP Paysan-Lafosse Typhaine T Pesseat Sebastien S Potter Simon C SC Qureshi Matloob A MA Rawlings Neil D ND Redaschi Nicole N Richardson Lorna J LJ Rivoire Catherine C Salazar Gustavo A GA Sangrador-Vegas Amaia A Sigrist Christian J A CJA Sillitoe Ian I Sutton Granger G GG Thanki Narmada N Thomas Paul D PD Tosatto Silvio C E SCE Yong Siew-Yit SY Finn Robert D RD

Nucleic acids research 20190101 D1

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 in ...[more]

PMID: 30398656

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Project description:Protein structure is connected with its function and interaction and plays an extremely important role in protein characterization. As one of the most important analytical methods for protein characterization, Proteomics is widely used to determine protein composition, quantitation, interaction, and even structures. However, due to the gap between identified proteins by proteomics and available 3D structures, it was very challenging, if not impossible, to visualize proteomics results in 3D and further explore the structural aspects of proteomics experiments. Recently, two groups of researchers from DeepMind and Baker lab have independently published protein structure prediction tools that can help us obtain predicted protein structures for the whole human proteome. Although there is still debate on the validity of some of the predicted structures, it is no doubt that these represent the most accurate predictions to date. More importantly, this enabled us to visualize the majority of human proteins for the first time. To help other researchers best utilize these protein structure predictions, we present the Sequence Coverage Visualizer (SCV), http://scv.lab.gy, a web application for protein sequence coverage 3D visualization. Here we showed a few possible usages of the SCV, including the labeling of post-translational modifications and isotope labeling experiments. These results highlight the usefulness of such 3D visualization for proteomics experiments and how SCV can turn a regular result list into structural insights. Furthermore, when used together with limited proteolysis, we demonstrated that SCV can help validate and compare different protein structures, including predicted ones and existing PDB entries. By performing limited proteolysis on native proteins at various time points, SCV can visualize the progress of the digestion. This time-series data further allowed us to compare the predicted structure and existing PDB entries. Although not deterministic, these comparisons could be used to refine current predictions further and represent an important step towards a complete and correct protein structure database. Overall, SCV is a convenient and powerful tool for visualizing proteomics results.

Dataset Information

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

Publications

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

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