{"id":1878,"date":"2022-07-29T12:04:27","date_gmt":"2022-07-29T12:04:27","guid":{"rendered":"http:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/?page_id=1878"},"modified":"2023-03-11T21:29:06","modified_gmt":"2023-03-11T21:29:06","slug":"ht3-l4-programmatic-access-of-macromolecular-structure-data","status":"publish","type":"page","link":"https:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/ht3-l4-programmatic-access-of-macromolecular-structure-data\/","title":{"rendered":"HT3 L4: Programmatic access of macromolecular structure data"},"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=\"179\" height=\"179\" 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: 179px) 100vw, 179px\" \/><\/strong><\/p>\n<h4>L4 (Lecture): Programmatic access of macromolecular structure data<\/h4>\n<p>&nbsp;<\/p>\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;\">If you are looking to access large volumes of PDB data for your own analyses, the best way for quick and automated access is to do it programmatically, instead of going through the website. PDBe has developed a set of REST APIs that provide easy access to high-quality information regarding biomacromolecular structures archived in PDB.<\/span><\/p>\n<p style=\"text-align: justify;\">&nbsp;<\/p>\n<p style=\"text-align: justify;\"><strong>These APIs provide a simple, reliable, lightweight mechanism to:<\/strong><\/p>\n<ul style=\"text-align: justify;\">\n<li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Query macromolecular structure data<\/span><\/li>\n<li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Select entries or molecules of interest and access targeted information about them<\/span><\/li>\n<li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Access information on the molecules, experimental details, assemblies, motifs, function, taxonomy, structure quality, etc.<\/span><\/li>\n<\/ul>\n<p style=\"text-align: justify;\">&nbsp;<\/p>\n<p style=\"text-align: justify;\"><span style=\"font-weight: 400;\">There is more information on the various PDBe APIs at <a href=\"http:\/\/pdbe.org\/api\">pdbe.org\/api<\/a><\/span><\/p>\n<p style=\"text-align: justify;\">&nbsp;<\/p>\n<p style=\"text-align: justify;\"><span style=\"font-weight: 400;\">PDBe also has a dedicated webinar series on programmatic access:<\/span><\/p>\n<p style=\"text-align: justify;\"><a href=\"http:\/\/pdbeurope.github.io\/api-webinars\"><span style=\"font-weight: 400;\">pdbeurope.github.io\/api-webinars<\/span><\/a><\/p>\n<p style=\"text-align: justify;\">&nbsp;<\/p>\n<p style=\"text-align: justify;\"><span style=\"font-weight: 400;\">This talk will give an introduction to how to programmatically access data in the PDB. It will also highlight how this data is used on PDBe and PDBe-KB pages as a case study for the use of the PDBe APIs. It will also introduce the PDB component library which provides access to web components developed by PDBe to visualize structural data.<\/span><\/p>\n<p style=\"text-align: justify;\">&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>HT3: Databases L4 (Lecture): Programmatic access of macromolecular structure data &nbsp; David Armstrong Protein Data Bank in Europe (PDBe) European Bioinformatics Institute (EMBL-EBI) E-mail: davida@ebi.ac.uk If you are looking to access large volumes of PDB data for your own analyses, the best way for quick and automated access is to do it programmatically, instead of [&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-1878","page","type-page","status-publish","hentry"],"aioseo_notices":[],"aioseo_head":"\n\t\t<!-- All in One SEO 5.0.2.1 - aioseo.com -->\n\t<meta name=\"description\" content=\"HT3: Databases L4 (Lecture): Programmatic access of macromolecular structure data David Armstrong Protein Data Bank in Europe (PDBe) European Bioinformatics Institute (EMBL-EBI) E-mail: davida@ebi.ac.uk If you are looking to access large volumes of PDB data for your own analyses, the best way for quick and automated access is to do it programmatically, instead of\" \/>\n\t<meta name=\"robots\" content=\"max-image-preview:large\" \/>\n\t<link rel=\"canonical\" href=\"https:\/\/hrvatska-udruga-kristalografa.hr\/htcc5\/ht3-l4-programmatic-access-of-macromolecular-structure-data\/\" \/>\n\t<meta name=\"generator\" content=\"All in One SEO (AIOSEO) 5.0.2.1\" \/>\n\t\t<meta property=\"og:locale\" content=\"en_US\" \/>\n\t\t<meta property=\"og:site_name\" content=\"HTCC5 - 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