{"id":1872,"date":"2022-07-29T11:51:50","date_gmt":"2022-07-29T11:51:50","guid":{"rendered":"http:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/?page_id=1872"},"modified":"2023-03-11T21:25:40","modified_gmt":"2023-03-11T21:25:40","slug":"ht3-l2-pdbe-knowledge-base-pdbe-kb-changing-the-context-of-structure-data","status":"publish","type":"page","link":"https:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/ht3-l2-pdbe-knowledge-base-pdbe-kb-changing-the-context-of-structure-data\/","title":{"rendered":"HT3 L2: PDBe Knowledge-Base (PDBe-KB): Changing the context of structure data"},"content":{"rendered":"

HT3: Databases\"\"<\/strong><\/p>\n

L2 (Lecture): PDBe Knowledge-Base (PDBe-KB): Changing the context of structure data<\/h4>\n

 <\/p>\n

David Armstrong<\/strong>
\nProtein Data Bank in Europe (PDBe)
\nEuropean Bioinformatics Institute (EMBL-EBI)
\nE-mail: davida@ebi.ac.uk<\/p>\n

 <\/p>\n

This talk will give participants an introduction to the PDBe Knowledge Base (PDBe-KB), a community-driven resource managed by the PDBe team, collating functional annotations and predictions for structure data in the PDB archive. PDBe-KB is a flagship of the ELIXIR 3D-BioInfo Community (elixir-europe.org\/communities\/3d-bioinfo), an international group of researchers and software developers working on improving the use of macromolecular structure data in life science research. The 3D-Beacons network (3d-beacons.org), a vital part of the PDBe-KB consortium activities, provides integrated access to experimental and computational protein structure models.<\/span><\/p>\n

 <\/p>\n

PDBe-KB aims to:<\/span><\/h4>\n
    \n
  • Implement a comprehensive, FAIR<\/span> infrastructure for macromolecular structures and their annotations<\/span><\/li>\n
  • Enrich macromolecular structure data with structural and functional annotations to establish their biological context<\/span><\/li>\n
  • Develop innovative tools for data access and visualization<\/span><\/li>\n
  •  <\/li>\n<\/ul>\n

    Aggregated Views<\/span><\/h4>\n

    PDBe-KB Aggregated Views are a set of web pages that aggregate all the structural and functional data for a specific molecular entity. There are many possible and valuable ways to aggregate data, for example by proteins, domains, small molecules, or macromolecular complexes.<\/span><\/p>\n

     <\/p>\n

    Aggregated Views of Proteins<\/span><\/h4>\n

    The PDBe-KB Aggregated View of proteins provides a comprehensive overview of structural data available in the PDB for a full-length protein sequence (i.e. UniProt accession). Either PDB identifiers or UniProt accessions can be used to display all the available data for a given protein. The webpages display a list of PDB entries containing the protein, small and macromolecules and their interaction sites with the given protein, and additional functional annotations, such as sequence conservation and druggable sites.<\/span><\/p>\n

     <\/p>\n

    View the PDBe-KB Aggregated Views at pdbekb.org\/proteins<\/span><\/p>\n

    3D-Beacons Network<\/span><\/h4>\n

    3D-Beacons Network is an open collaboration between providers of macromolecular structure models. The 3D-Beacons portal is a unified platform that provides access to model coordinates and meta-information from all the contributing data resources in a standardized data format.<\/span><\/p>\n

     <\/p>\n

    The 3D-Beacons portal allows users to search using UniProt accessions and see all the available experimental and computational models from the member data providers. The PDBe-KB Aggregated Views of proteins display these structures for a protein of interest.<\/span><\/p>\n

     <\/p>\n

    View the 3D-Beacons Network website at 3d-beacons.org.<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"

    HT3: Databases L2 (Lecture): PDBe Knowledge-Base (PDBe-KB): Changing the context of structure data   David Armstrong Protein Data Bank in Europe (PDBe) European Bioinformatics Institute (EMBL-EBI) E-mail: davida@ebi.ac.uk   This talk will give participants an introduction to the PDBe Knowledge Base (PDBe-KB), a community-driven resource managed by the PDBe team, collating functional annotations and predictions […]<\/p>\n","protected":false},"author":2,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"ngg_post_thumbnail":0,"footnotes":""},"class_list":["post-1872","page","type-page","status-publish","hentry"],"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/wp-json\/wp\/v2\/pages\/1872","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/wp-json\/wp\/v2\/comments?post=1872"}],"version-history":[{"count":2,"href":"https:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/wp-json\/wp\/v2\/pages\/1872\/revisions"}],"predecessor-version":[{"id":2458,"href":"https:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/wp-json\/wp\/v2\/pages\/1872\/revisions\/2458"}],"wp:attachment":[{"href":"https:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/wp-json\/wp\/v2\/media?parent=1872"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}