{"id":1659,"date":"2023-11-10T13:48:51","date_gmt":"2023-11-10T13:48:05","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/training\/materials\/structural-bioinformatics-materials-temp-2023v2\/day-4\/alphafold\/"},"modified":"2026-01-12T14:18:23","modified_gmt":"2026-01-12T14:18:23","slug":"alphafold-database-and-colabfold","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/materials\/structural-bioinformatics-materials\/protein-structure-prediction-and-molecular-docking\/alphafold-database-and-colabfold\/","title":{"rendered":"AlphaFold Database and ColabFold"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\"><strong>Trainer:<\/strong> Paulyna Maga\u00f1a<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Overview:<\/strong> This session will give you an introduction to AlphaFold including: <\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Why AlphaFold?<\/li>\n\n\n\n<li>High-level overview of AlphaFold<\/li>\n\n\n\n<li>AlphaFold Multimer<\/li>\n\n\n\n<li>ColabFold<\/li>\n\n\n\n<li>Impact of AlphaFold<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Learning outcomes:<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">By the end of this session you will be able to:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Describe AlphaFold and its use in generating predicted protein structures<\/li>\n\n\n\n<li>Run ColabFold and view results<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Materials<\/strong>:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Link to presentation <a href=\"https:\/\/ftp.ebi.ac.uk\/pub\/training\/2023\/Structural_bioinformatics_2023\/Day_4\/AlphaFold\/AlphaFold.pptx\" target=\"_blank\" rel=\"noreferrer noopener\">slides<\/a> and <a href=\"https:\/\/ftp.ebi.ac.uk\/pub\/training\/2025\/Structural_bioinformatics_2025\/Day_3\/StructBio2025_AlphaFold.pdf\" target=\"_blank\" rel=\"noreferrer noopener\">PDF<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/ftp.ebi.ac.uk\/pub\/training\/2025\/Structural_bioinformatics_2025\/Day_3\/StructBio2025_AlphaFold%20Database.pdf\">AlphaFold Database slides<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/ftp.ebi.ac.uk\/pub\/training\/2023\/Structural_bioinformatics_2023\/Day_4\/AlphaFold\/\" target=\"_blank\" rel=\"noreferrer noopener\">Link to data folder<\/a><\/li>\n<\/ul>\n\n\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">2022 edition recording:<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n\n\n\n<iframe loading=\"lazy\" src=\"https:\/\/embl-ebi.cloud.panopto.eu\/Panopto\/Pages\/Embed.aspx?id=1a1bc37c-55e0-475b-ac6c-af33010ca1e5&amp;autoplay=false&amp;offerviewer=true&amp;showtitle=true&amp;showbrand=true&amp;captions=false&amp;interactivity=all\" height=\"405\" width=\"720\" style=\"border: 1px solid #464646;\" allowfullscreen=\"\" allow=\"autoplay\" aria-label=\"Panopto Embedded Video Player\"><\/iframe>\n\n\n\n<h2 class=\"wp-block-heading\">Alphafold database<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Trainer:<\/strong> Paulyna Maga\u00f1a<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Overview:<\/strong> <br>This session will go through: <\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>What data do we store?<\/li>\n\n\n\n<li>Evaluate predicted structures from the AlphaFold Database (AFD)<\/li>\n\n\n\n<li>Different ways to access the database<\/li>\n\n\n\n<li>Current developments<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Learning outcomes:<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">By the end of this session you will be able to:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Navigate the AlphaFold Database to search for and assess predicted protein structures.<\/li>\n\n\n\n<li>Define the use of 3D-Beacons in structural biology.<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Materials: <\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/ftp.ebi.ac.uk\/pub\/training\/2022\/Structural_Bioinformatics_2022\/Day%203\/AlphaFold%20DB%20_%203D-Beacons.pptx\" target=\"_blank\" rel=\"noreferrer noopener\">Link to 2022 presentation slides<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/ftp.ebi.ac.uk\/pub\/training\/2023\/Structural_bioinformatics_2023\/Day_4\/AlphaFold\/AFDB.pptx\" target=\"_blank\" rel=\"noreferrer noopener\">Link to 2023 presentation slides<\/a> and <a href=\"https:\/\/ftp.ebi.ac.uk\/pub\/training\/2023\/Structural_bioinformatics_2023\/Day_4\/AlphaFold\/AFDB.pptx\" target=\"_blank\" rel=\"noreferrer noopener\">PDF<\/a><\/li>\n\n\n\n<li>Link to tutorial <a href=\"https:\/\/ftp.ebi.ac.uk\/pub\/training\/2023\/Structural_bioinformatics_2023\/Day_4\/AlphaFold\/AlphaFold%20tutorial%20-%20structure.pdf\" target=\"_blank\" rel=\"noreferrer noopener\">PDF<\/a> and <a href=\"https:\/\/ftp.ebi.ac.uk\/pub\/training\/2023\/Structural_bioinformatics_2023\/Day_4\/AlphaFold\/AlphaFold%20tutorial%20-%20structure.docx\" target=\"_blank\" rel=\"noreferrer noopener\">document<\/a><\/li>\n\n\n\n<li>Recorded lecture: <\/li>\n<\/ul>\n\n\n\n<iframe loading=\"lazy\" src=\"https:\/\/embl-ebi.cloud.panopto.eu\/Panopto\/Pages\/Embed.aspx?id=9e8fcaef-dd84-45e4-9e19-af33010c129f&amp;autoplay=false&amp;offerviewer=true&amp;showtitle=true&amp;showbrand=true&amp;captions=false&amp;interactivity=all\" height=\"405\" width=\"720\" style=\"border: 1px solid #464646;\" allowfullscreen=\"\" allow=\"autoplay\" aria-label=\"Panopto Embedded Video Player\"><\/iframe>\n","protected":false},"excerpt":{"rendered":"<p>Trainer: Paulyna Maga\u00f1a Overview: This session will give you an introduction to AlphaFold including: Learning outcomes: By the end of this session you will be able to: Materials: 2022 edition recording: Alphafold database Trainer: Paulyna Maga\u00f1a Overview: This session will go through: Learning outcomes: By the end of this session you will be able to:&#8230;<\/p>\n","protected":false},"author":32,"featured_media":0,"parent":15,"menu_order":3,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-1659","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/structural-bioinformatics-materials\/wp-json\/wp\/v2\/pages\/1659","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/structural-bioinformatics-materials\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/structural-bioinformatics-materials\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/structural-bioinformatics-materials\/wp-json\/wp\/v2\/users\/32"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/structural-bioinformatics-materials\/wp-json\/wp\/v2\/comments?post=1659"}],"version-history":[{"count":7,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/structural-bioinformatics-materials\/wp-json\/wp\/v2\/pages\/1659\/revisions"}],"predecessor-version":[{"id":1907,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/structural-bioinformatics-materials\/wp-json\/wp\/v2\/pages\/1659\/revisions\/1907"}],"up":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/structural-bioinformatics-materials\/wp-json\/wp\/v2\/pages\/15"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/structural-bioinformatics-materials\/wp-json\/wp\/v2\/media?parent=1659"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}