{"id":11769,"date":"2017-12-06T14:53:12","date_gmt":"2017-12-06T13:53:12","guid":{"rendered":"https:\/\/news.embl.de\/?p=11769"},"modified":"2024-03-22T11:52:21","modified_gmt":"2024-03-22T10:52:21","slug":"exploring-3d-macromolecules","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/exploring-3d-macromolecules\/","title":{"rendered":"Exploring 3D macromolecules in a flash"},"content":{"rendered":"\n<p><a href=\"https:\/\/www.ebi.ac.uk\/pdbe\/\" target=\"_blank\" rel=\"noopener noreferrer\">EMBL-EBI\u2019s Protein Data Bank in Europe (PDBe)<\/a> has updated its 3D viewer, enabling users to load 3D protein structures instantly on any Internet-connected device. The upgrade particularly benefits researchers working in areas with low Internet speed. The new viewer is also mobile-friendly, allowing anyone who is interested in biology to explore the beauty and mystery of proteins and other macromolecules.<\/p>\n\n\n\n<p>PDBe prides itself on being the European resource for collecting, organising and sharing data on molecular structures, such as proteins. These \u2018macromolecules\u2019 include proteins and nucleic acids, plus carbohydrates, lipids and drug molecules represented in more than 130,000 PDB entries. The team also develops free analytical tools to make structure-related data more and more accessible to the biomedical community.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Macro molecules, massive files<\/h2>\n\n\n\n<p>Some of PDBe\u2019s 3D structures, are huge, notably those solved by electron microscopy, for which the Nobel Prize was awarded recently. Nevertheless, each detail is visible and easy to explore. Delivering this amount of detail comes with a price. Files can exceed a gigabyte, so they load very slowly, especially on older machines or in areas with poor Internet connectivity. This also makes the structures hard to view on devices such as mobile phones or tablets.<\/p>\n\n\n\n<p>To tackle this challenge, the PDBe team, working closely with scientists from the <a href=\"https:\/\/www.ceitec.eu\/\" target=\"_blank\" rel=\"noopener noreferrer\">Central European Institute of Technology (CEITEC)<\/a> in the Czech Republic, has implemented a compression format that reduces the size of files up to 500 times. The new viewer, LiteMol Suite, also uses a technique employed in virtual reality and gaming, which involves downloading only essential data, such as one section of a protein, or a small part of the experimental data, instead of the whole file.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">A world of wonder<\/h2>\n\n\n\n<p>\u201cSeeing the intricate patterns of a virus or visualising how a pain-killing drug works are unique experiences that have traditionally needed specialised software,\u201d explains <a href=\"https:\/\/www.ebi.ac.uk\/about\/people\/matthew-conroy\" target=\"_blank\" rel=\"noopener noreferrer\">Matthew Conroy, Scientific Curator at PDBe<\/a>. \u201cPublic databases and visualisation tools are becoming much more accessible, which means the biological wonders we work with are open to a much wider audience.\u201d<\/p>\n\n\n\n<p>The PDBe team hopes that the implementation of LiteMol will encourage more people \u2013 including teachers and pupils \u2013 to explore EMBL-EBI\u2019s free structural data resources.<\/p>\n\n\n\n<p>\u201cIn the UK, students as young as 13 are studying proteins as part of the science curriculum,\u201d continues Conroy. \u201cPDBe\u2019s new viewer could support classroom teaching, giving students a chance to actually see a protein\u2019s structure in 3D, play around with it, zoom in and explore.\u201d<\/p>\n\n\n\n<p>For a more detailed look at PDBe\u2019s interactive, web-based visualisation of large-scale macromolecular structure data, read the <a href=\"https:\/\/www.nature.com\/articles\/nmeth.4499.epdf?author_access_token=ArzsKX1Pi-BBAQv4g7xyU9RgN0jAjWel9jnR3ZoTv0PAwDYbZ0Uj0uiWbMK0BEkiT1bcITEAfDfZhtnbastR43WXPyY0M60TqntfnbgGHjTmYwdJswMtxkMEiZstmrfg\" target=\"_blank\" rel=\"noopener noreferrer\">team\u2019s recent paper<\/a> in <em>Nature Methods<\/em>.<\/p>\n\n\n\n<p>This post was originally published on <a href=\"https:\/\/www.ebi.ac.uk\/about\/news\/announcement\/pdbe-new-3d-viewer\" target=\"_blank\" rel=\"canonical nofollow noopener noreferrer\" data-href=\"https:\/\/www.ebi.ac.uk\/about\/news\/announcement\/pdbe-new-3d-viewer\">EMBL-EBI News.<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>High resolution 3D protein structures in a giffy with PDBe<\/p>\n","protected":false},"author":47,"featured_media":11772,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[2,17591],"tags":[28,36,546,188,76],"embl_taxonomy":[],"class_list":["post-11769","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science","category-science-technology","tag-bioinformatics","tag-embl-ebi","tag-mole","tag-protein-data-bank","tag-service"],"acf":{"article_intro":"<p>New techniques from gaming allow users to load giant 3D protein images quickly in PDBe<\/p>\n","related_links":[{"link_description":"Protein Data Bank in Europe","link_url":"https:\/\/www.ebi.ac.uk\/pdbe\/"},{"link_description":"Central European Institute of Technology (CEITEC)","link_url":"https:\/\/www.ceitec.eu\/"}],"article_sources":[{"source_description":"<p>SEHNAL, D.\u00a0<em>et al<\/em>.\u00a0<em>Nature Methods<\/em>, vol. 14, no 12. DOI: 10.1038\/nmeth.4499<\/p>\n","source_link_url":"https:\/\/www.nature.com\/articles\/nmeth.4499.epdf?author_access_token=ArzsKX1Pi-BBAQv4g7xyU9RgN0jAjWel9jnR3ZoTv0PAwDYbZ0Uj0uiWbMK0BEkiT1bcITEAfDfZhtnbastR43WXPyY0M60TqntfnbgGHjTmYwdJswMtxkMEiZstmrfg"}],"vf_locked":false,"featured":false,"color":"#007B53"},"embl_taxonomy_terms":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Exploring 3D protein structures in a flash<\/title>\n<meta name=\"description\" content=\"New techniques from gaming allow users to load giant 3D protein structures quickly in the Protein Data Bank in Europe (PDBe).\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.embl.org\/news\/science\/exploring-3d-macromolecules\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Exploring 3D protein structures in a flash\" \/>\n<meta property=\"og:description\" content=\"New techniques from gaming allow users to load giant 3D protein structures quickly in the Protein Data Bank in Europe (PDBe).\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.embl.org\/news\/science\/exploring-3d-macromolecules\/\" \/>\n<meta property=\"og:site_name\" content=\"EMBL\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/embl.org\/\" \/>\n<meta property=\"article:published_time\" content=\"2017-12-06T13:53:12+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2024-03-22T10:52:21+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2017\/12\/PDBe_New_viewer_EMBL620x425-1-e1512400496209.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"620\" \/>\n\t<meta property=\"og:image:height\" content=\"425\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"author\" content=\"Oana Stroe\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@embl\" \/>\n<meta name=\"twitter:site\" content=\"@embl\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Oana Stroe\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"2 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"NewsArticle\",\"@id\":\"https:\/\/www.embl.org\/news\/science\/exploring-3d-macromolecules\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/exploring-3d-macromolecules\/\"},\"author\":{\"name\":\"Oana Stroe\",\"@id\":\"https:\/\/www.embl.org\/news\/#\/schema\/person\/95d28f359cc138357c5dcf79319ef414\"},\"headline\":\"Exploring 3D macromolecules in a flash\",\"datePublished\":\"2017-12-06T13:53:12+00:00\",\"dateModified\":\"2024-03-22T10:52:21+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/exploring-3d-macromolecules\/\"},\"wordCount\":448,\"publisher\":{\"@id\":\"https:\/\/www.embl.org\/news\/#organization\"},\"image\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/exploring-3d-macromolecules\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2017\/12\/PDBe_New_viewer_EMBL620x425-1-e1512400496209.jpg\",\"keywords\":[\"bioinformatics\",\"embl-ebi\",\"mole\",\"protein data bank\",\"service\"],\"articleSection\":[\"Science\",\"Science &amp; 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