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RCSB Protein Data Bank 1D Tools and Services.

ABSTRACT: Interoperability between polymer sequences and structural data is essential for providing a complete picture of protein and gene features and helping to understand biomolecular function. Herein, we present two resources designed to improve interoperability between the RCSB Protein Data Bank, the NCBI, and the UniProtKB data resources and visualize integrated data therefrom. The underlying tools provide a flexible means of mapping between the different coordinate spaces and an interactive tool allows convenient visualization of the 1-dimensional data over the web. https://1d-coordinates.rcsb.org and https://rcsb.github.io/rcsb-saguaro. Supplementary data are available at Bioinformatics online.

SUBMITTER: Segura J

PROVIDER: S-EPMC8016458 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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RCSB Protein Data Bank 1D tools and services.

Segura Joan J Rose Yana Y Westbrook John J Burley Stephen K SK Duarte Jose M JM

Bioinformatics (Oxford, England) 20210401 22-23

<h4>Motivation</h4>Interoperability between polymer sequences and structural data is essential for providing a complete picture of protein and gene features and helping to understand biomolecular function.<h4>Results</h4>Herein, we present two resources designed to improve interoperability between the RCSB Protein Data Bank, the NCBI and the UniProtKB data resources and visualize integrated data therefrom. The underlying tools provide a flexible means of mapping between the different coordinate ...[more]

PMID: 33313665

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Project description:BACKGROUND: Biological data have traditionally been stored and made publicly available through a variety of on-line databases, whereas biological knowledge has traditionally been found in the printed literature. With journals now on-line and providing an increasing amount of open access content, often free of copyright restriction, this distinction between database and literature is blurring. To exploit this opportunity we present the integration of open access literature with the RCSB Protein Data Bank (PDB). RESULTS: BioLit provides an enhanced view of articles with markup of semantic data and links to biological databases, based on the content of the article. For example, words matching to existing biological ontologies are highlighted and database identifiers are linked to their database of origin. Among other functions, it identifies PDB IDs that are mentioned in the open access literature, by parsing the full text for all research articles in PubMed Central (PMC) and exposing the results as simple XML Web Services. Here, we integrate BioLit results with the RCSB PDB website by using these services to find PDB IDs that are mentioned in research articles and subsequently retrieving abstract, figures, and text excerpts for those articles. A new RCSB PDB literature view permits browsing through the figures and abstracts of the articles that mention a given structure. The BioLit Web Services that are providing the underlying data are publicly accessible. A client library is provided that supports querying these services (Java). CONCLUSIONS: The integration between literature and websites, as demonstrated here with the RCSB PDB, provides a broader view for how a given structure has been analyzed and used. This approach detects the mention of a PDB structure even if it is not formally cited in the paper. Other structures related through the same literature references can also be identified, possibly providing new scientific insight. To our knowledge this is the first time that database and literature have been integrated in this way and it speaks to the opportunities afforded by open and free access to both database and literature content.

Dataset Information

RCSB Protein Data Bank 1D Tools and Services.

Publications

RCSB Protein Data Bank 1D tools and services.

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