Dataset Information

The RCSB protein data bank: integrative view of protein, gene and 3D structural information.

ABSTRACT: The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb.org), the US data center for the global PDB archive, makes PDB data freely available to all users, from structural biologists to computational biologists and beyond. New tools and resources have been added to the RCSB PDB web portal in support of a 'Structural View of Biology.' Recent developments have improved the User experience, including the high-speed NGL Viewer that provides 3D molecular visualization in any web browser, improved support for data file download and enhanced organization of website pages for query, reporting and individual structure exploration. Structure validation information is now visible for all archival entries. PDB data have been integrated with external biological resources, including chromosomal position within the human genome; protein modifications; and metabolic pathways. PDB-101 educational materials have been reorganized into a searchable website and expanded to include new features such as the Geis Digital Archive.

SUBMITTER: Rose PW

PROVIDER: S-EPMC5210513 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature

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The RCSB protein data bank: integrative view of protein, gene and 3D structural information.

Rose Peter W PW Prlić Andreas A Altunkaya Ali A Bi Chunxiao C Bradley Anthony R AR Christie Cole H CH Costanzo Luigi Di LD Duarte Jose M JM Dutta Shuchismita S Feng Zukang Z Green Rachel Kramer RK Goodsell David S DS Hudson Brian B Kalro Tara T Lowe Robert R Peisach Ezra E Randle Christopher C Rose Alexander S AS Shao Chenghua C Tao Yi-Ping YP Valasatava Yana Y Voigt Maria M Westbrook John D JD Woo Jesse J Yang Huangwang H Young Jasmine Y JY Zardecki Christine C Berman Helen M HM Burley Stephen K SK

Nucleic acids research 20161027 D1

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb.org), the US data center for the global PDB archive, makes PDB data freely available to all users, from structural biologists to computational biologists and beyond. New tools and resources have been added to the RCSB PDB web portal in support of a 'Structural View of Biology.' Recent developments have improved the User experience, including the high-speed NGL Viewer that provides 3D molecular visua ...[more]

PMID: 27794042

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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

The RCSB protein data bank: integrative view of protein, gene and 3D structural information.

Publications

The RCSB protein data bank: integrative view of protein, gene and 3D structural information.

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