{"id":1874,"date":"2022-07-29T11:55:27","date_gmt":"2022-07-29T11:55:27","guid":{"rendered":"http:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/?page_id=1874"},"modified":"2023-03-11T21:26:36","modified_gmt":"2023-03-11T21:26:36","slug":"ht3-t2-analysing-large-scale-pdb-data-using-pdbe-kb","status":"publish","type":"page","link":"https:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/ht3-t2-analysing-large-scale-pdb-data-using-pdbe-kb\/","title":{"rendered":"HT3 T2: Analysing large scale PDB data using PDBe-KB"},"content":{"rendered":"<p><strong>HT3: Databases<img loading=\"lazy\" decoding=\"async\" class=\"wp-image-1908 alignright\" src=\"http:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/wp-content\/uploads\/2022\/07\/armstrong-300x300.jpg\" alt=\"\" width=\"177\" height=\"177\" srcset=\"https:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/wp-content\/uploads\/2022\/07\/armstrong-300x300.jpg 300w, https:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/wp-content\/uploads\/2022\/07\/armstrong-150x150.jpg 150w, https:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/wp-content\/uploads\/2022\/07\/armstrong-400x400.jpg 400w, https:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/wp-content\/uploads\/2022\/07\/armstrong-100x100.jpg 100w, https:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/wp-content\/uploads\/2022\/07\/armstrong.jpg 510w\" sizes=\"auto, (max-width: 177px) 100vw, 177px\" \/><\/strong><\/p>\n<h4>T2 (Tutorial): Analysing large scale PDB data using PDBe-KB<\/h4>\n<p><strong>David Armstrong<\/strong><br \/>\nProtein Data Bank in Europe (PDBe)<br \/>\nEuropean Bioinformatics Institute (EMBL-EBI)<br \/>\nE-mail: davida@ebi.ac.uk<\/p>\n<p style=\"text-align: justify;\"><span style=\"font-weight: 400;\">This hands-on session will demonstrate how users can perform a detailed analysis of PDB data using the aggregated views from PDBe-KB. These pages contain extensive data on protein structures, their binding site, and binding partners that can be used to support research. The information on these pages comes from the analysis of data in the PDB archive but also integrates data from other resources including curated and predicted functional annotations.<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"font-weight: 400;\">The tutorial will include sections on interpreting ligand binding sites, identifying macromolecular interactions, and the access of superimposed structures. All this data and more is accessible through the PDBe-KB Aggregated Views of Proteins and freely available to access and download.<\/span><\/p>\n<p>&nbsp;<\/p>\n<h4 style=\"text-align: justify;\"><b>Learning outcomes<\/b><\/h4>\n<ul>\n<li style=\"font-weight: 400; text-align: justify;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Access the PDBe-KB aggregated views to view all structural data for a specific protein<\/span><\/li>\n<li style=\"font-weight: 400; text-align: justify;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Interpret ligand binding sites and macromolecular interactions to determine important functional amino acids<\/span><\/li>\n<li style=\"font-weight: 400; text-align: justify;\" aria-level=\"1\"><span style=\"font-weight: 400;\">View superimposed protein structures and ligand binding sites to identify key regions and assess structural variability<\/span><\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>HT3: Databases T2 (Tutorial): Analysing large scale PDB data using PDBe-KB David Armstrong Protein Data Bank in Europe (PDBe) European Bioinformatics Institute (EMBL-EBI) E-mail: davida@ebi.ac.uk This hands-on session will demonstrate how users can perform a detailed analysis of PDB data using the aggregated views from PDBe-KB. These pages contain extensive data on protein structures, their [&hellip;]<\/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-1874","page","type-page","status-publish","hentry"],"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/wp-json\/wp\/v2\/pages\/1874","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=1874"}],"version-history":[{"count":2,"href":"https:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/wp-json\/wp\/v2\/pages\/1874\/revisions"}],"predecessor-version":[{"id":2460,"href":"https:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/wp-json\/wp\/v2\/pages\/1874\/revisions\/2460"}],"wp:attachment":[{"href":"https:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/wp-json\/wp\/v2\/media?parent=1874"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}