{"id":896,"date":"2022-04-07T14:57:05","date_gmt":"2022-04-07T14:57:05","guid":{"rendered":"https:\/\/www.embl.org\/about\/info\/annual-report\/?page_id=896"},"modified":"2022-06-09T13:00:21","modified_gmt":"2022-06-09T13:00:21","slug":"alphafold-a-game-changer-for-structural-biology","status":"publish","type":"page","link":"https:\/\/www.embl.org\/about\/info\/annual-report\/ar2021\/alphafold-a-game-changer-for-structural-biology","title":{"rendered":"AlphaFold: a game-changer for structural biology"},"content":{"rendered":"\n\n  <style>\n    .vf-hero {\n              --vf-hero--bg-image: url('https:\/\/www.embl.org\/about\/info\/annual-report\/wp-content\/uploads\/2022\/05\/20220524_AR2021_banners-scaled.jpg');\n            }\n\n  <\/style>\n<section id=\"\" class=\"vf-hero | vf-u-fullbleed  | vf-u-margin__bottom--0\">\n  <div class=\"vf-hero__content | vf-box | vf-stack vf-stack--400\">\n        <h1 class=\"vf-hero__heading\">\n              Annual Report 2021          <\/h1>\n\n        <p class=\"vf-hero__subheading\">A year of exceptional life science research, training, service, industry collaboration, and integration of European life science research.<\/p>\n    \n    \n      <\/div>\n<\/section>\n<!--\/vf-hero-->\n\n\n\n<div class=\"vf-grid | vf-grid__col-3\"><div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<h1 class=\"wp-block-heading\">AlphaFold: a game-changer for structural biology<\/h1>\n\n\n\n<h2 class=\"wp-block-heading\">EMBL-EBI teams up with DeepMind to make breakthrough AI-powered protein structure predictions freely available to the world.<\/h2>\n\n\n\n<figure class=\"vf-figure wp-block-image size-full is-style-default\"><img loading=\"lazy\" decoding=\"async\" width=\"1000\" height=\"600\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/about\/info\/annual-report\/wp-content\/uploads\/2022\/04\/2021_AlphaFold_Thornton_Credit_Karen_Arnott_1000x600-m.jpg\" alt=\"Protein structures are depicted as colourful ribbons\" class=\"wp-image-619\" srcset=\"https:\/\/www.embl.org\/about\/info\/annual-report\/wp-content\/uploads\/2022\/04\/2021_AlphaFold_Thornton_Credit_Karen_Arnott_1000x600-m.jpg 1000w, https:\/\/www.embl.org\/about\/info\/annual-report\/wp-content\/uploads\/2022\/04\/2021_AlphaFold_Thornton_Credit_Karen_Arnott_1000x600-m-300x180.jpg 300w, https:\/\/www.embl.org\/about\/info\/annual-report\/wp-content\/uploads\/2022\/04\/2021_AlphaFold_Thornton_Credit_Karen_Arnott_1000x600-m-768x461.jpg 768w\" sizes=\"auto, (max-width: 1000px) 100vw, 1000px\" \/><figcaption class=\"vf-figure__caption\">Mouse-ear cress protein structure prediction from the AlphaFold database. Credit: EMBL<\/figcaption><\/figure>\n\n\n\n<p>Proteins play many roles in the biological world. They transport nutrients, trigger chemical reactions, and build the structures that make up all living things. To fully understand what a protein does, scientists need to know its 3D structure, and this is no easy task.<\/p>\n\n\n\n<p>Since the 1950s, scientists have used a range of methods to uncover hundreds of thousands of protein structures and made the data accessible through public archives. Building on these data,&nbsp; <a href=\"https:\/\/deepmind.com\/\">DeepMind<\/a> developed AlphaFold \u2013 an AI-powered system that can accurately predict millions of protein structures.<\/p>\n\n\n\n<p>In 2021, <a href=\"https:\/\/www.embl.org\/news\/science\/alphafold-database-launch\/\">EMBL-EBI and DeepMind<\/a> entered into a collaboration to develop and release the<a href=\"https:\/\/www.alphafold.ebi.ac.uk\/\"> AlphaFold Protein Structure Database<\/a>&nbsp; \u2013 an open platform where anyone can search, analyse, and download AlphaFold predictions.&nbsp;<\/p>\n\n\n\n<p>The beauty of AlphaFold is that it was trained using data from public resources \u2013 including the Protein Data Bank (PDB), UniProt, and MGnify, which are all co-hosted at EMBL-EBI. Building on EMBL-EBI\u2019s decades of data management expertise, DeepMind was able to quickly provide public access to AlphaFold predictions and crosslink them to existing data resources, making it much easier to discover them. DeepMind and EMBL-EBI are working to extend the database to over 100 million predictions.<\/p>\n\n\n\n<p>Many labs at EMBL and around the world have used the data to gain new insights into protein science:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Jan Kosinski at EMBL Hamburg used AlphaFold and electron cryo-microscopy data to build<a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.10.26.465776v1\"> a new model of the nuclear pore complex<\/a>, exemplifying how AlphaFold can support experimental structural biology to understand subcellular architecture.<\/li><li>Pedro Beltrao at EMBL-EBI and collaborators used AlphaFold to predict<a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.11.08.467664v1.full\"> complex protein interactions<\/a>, expanding understanding of human cell biology.&nbsp;<\/li><li>Jan Korbel at EMBL Heidelberg created a<a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.10.11.463937v1\"> <em>de novo<\/em> protein design framework<\/a> based on AlphaFold, which could help design new proteins for applications such as processing waste or degrading plastics.&nbsp;&nbsp;&nbsp;<\/li><\/ul>\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<div style=\"height:280px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--block | vf-u-margin__bottom--400\">\n\n    <img decoding=\"async\" width=\"200\" height=\"200\" src=\"https:\/\/www.embl.org\/about\/info\/annual-report\/wp-content\/uploads\/2022\/04\/JacquesDubochetCROPPED.jpg\" class=\"vf-profile__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/about\/info\/annual-report\/wp-content\/uploads\/2022\/04\/JacquesDubochetCROPPED.jpg 200w, https:\/\/www.embl.org\/about\/info\/annual-report\/wp-content\/uploads\/2022\/04\/JacquesDubochetCROPPED-150x150.jpg 150w\" sizes=\"auto, (max-width: 200px) 100vw, 200px\" \/>\n    <h3 class=\"vf-profile__title\" style=\"text-align: center;\">\n                                <\/h3>\n    \n    \n    \n      \n\n    \n<\/article>\n\n\n\n<p class=\"has-text-align-left vf-u-text-color--green vf-text--body vf-text-body--2\"><em>&#8220;I love that the collaboration between DeepMind and EMBL will make all the knowledge about protein structure open to all.&#8221;<\/em><\/p>\n\n\n\n<p class=\"has-text-align-left  vf-text--body vf-text-body--5\">\u2014 Jacques Dubochet, Nobel Laureate for Chemistry 2017; Group Leader at EMBL, 1978\u20131987<\/p>\n\n\n\n<article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--block | vf-u-margin__bottom--400\">\n\n    <img decoding=\"async\" width=\"220\" height=\"220\" src=\"https:\/\/www.embl.org\/about\/info\/annual-report\/wp-content\/uploads\/2022\/05\/CP-60022845.jpg\" class=\"vf-profile__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/about\/info\/annual-report\/wp-content\/uploads\/2022\/05\/CP-60022845.jpg 220w, https:\/\/www.embl.org\/about\/info\/annual-report\/wp-content\/uploads\/2022\/05\/CP-60022845-150x150.jpg 150w\" sizes=\"auto, (max-width: 220px) 100vw, 220px\" \/>\n    <h3 class=\"vf-profile__title\" style=\"text-align: center;\">\n                                <\/h3>\n    \n    \n    \n      \n\n    \n<\/article>\n\n\n\n<p class=\"has-text-align-left vf-u-text-color--green vf-text--body vf-text-body--2\"><meta charset=\"utf-8\"><em>&#8220;The EMBL-EBI and DeepMind collaboration that created the AlphaFold database is a big win for open science. Life sciences research will be able to make quantum jumps with this publicly accessible data.\u201d<\/em><\/p>\n\n\n\n<p class=\"has-text-align-left  vf-text--body vf-text-body--5\">\u2014 Mihaly Varadi, Project Leader, \u00a0<a href=\"https:\/\/www.ebi.ac.uk\/pdbe\/node\/1\">Protein Data Bank Europe <\/a>and <a href=\"https:\/\/alphafold.ebi.ac.uk\/\">AlphaFold Protein Structure Database<\/a><a href=\"https:\/\/www.ebi.ac.uk\/about\/teams\/pdbe\">, <\/a>EMBL-EBI<\/p>\n\n\n\n<article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--block | vf-u-margin__bottom--400\">\n\n    <img decoding=\"async\" width=\"155\" height=\"175\" src=\"https:\/\/www.embl.org\/about\/info\/annual-report\/wp-content\/uploads\/2022\/05\/CP-60025044-1.jpg\" class=\"vf-profile__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" \/>\n    <h3 class=\"vf-profile__title\" style=\"text-align: center;\">\n                                <\/h3>\n    \n    \n    \n      \n\n    \n<\/article>\n\n\n\n<p class=\"has-text-align-left vf-u-text-color--green vf-text--body vf-text-body--2\"><meta charset=\"utf-8\"><em>&#8220;Tools like AlphaFold require dedicated computing infrastructure to run, which takes a whole team to manage. I look forward to seeing how AlphaFold will give us new insights, e.g. into how neural networks can be applied to turbulence modelling \u2013 another large grey area on the science map.\u201d<\/em><\/p>\n\n\n\n<p class=\"has-text-align-left  vf-text--body vf-text-body--5\">\u2014 Jurij Pe\u010dar, HPC Engineer, <a href=\"https:\/\/www.embl.org\/about\/info\/it-services\/\">IT services at EMBL Heidelberg<\/a><\/p>\n\n\n\n<div class=\"vf-box vf-box--easy vf-box-theme--tertiary | vf-u-margin__bottom--400\">\n      <h3 class=\"vf-box__heading\">\n                Explore more 2021 EMBL structural database highlights:                  <\/h3> \n        <p class=\"vf-box__text\"><!-- wp:list --><\/p>\n<ul>\n<li style=\"font-weight: 400\"><a href=\"https:\/\/www.embl.org\/news\/science\/alphafold-database-launch\/\"><span style=\"font-weight: 400\">DeepMind and EMBL release the most complete database of predicted 3D structures of human proteins<\/span><\/a><\/li>\n<li style=\"font-weight: 400\"><a href=\"https:\/\/www.embl.org\/news\/science\/thornton-alphafold\/\"><span style=\"font-weight: 400\">Accessible 3D protein models to accelerate scientific discovery<\/span><\/a><\/li>\n<li style=\"font-weight: 400\"><a href=\"https:\/\/www.embl.org\/news\/science\/ai-protein-prediction-breakthrough\/\"><span style=\"font-weight: 400\">Artificial intelligence \u2014 a scientific game changer in 2021<\/span><\/a><\/li>\n<\/ul>\n<p class=\"vf-box__text\"><!-- \/wp:list --><\/p>\n<\/div>\n\n\n\n<h3 class=\"wp-block-heading\">References<\/h3>\n\n\n\n<p class=\"vf-text--body vf-text-body--5\">Mosalaganti S <em>et al. <\/em>(2021). <a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.10.26.465776v3.article-info\">Artificial intelligence reveals nuclear pore complexity<\/a>. <em>bioRxiv, <\/em>2 November 2021. DOI: 10.1101\/2021.10.26.465776<\/p>\n\n\n\n<p class=\"vf-text--body vf-text-body--5\">Burke DF <em>et al. <\/em>(2021). <a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.11.08.467664v1.full\">Towards a structurally resolved human protein interaction network<\/a>. <em>bioRxiv, <\/em>9 November 2021. DOI: 10.1101\/2021.11.08.467664<\/p>\n\n\n\n<p class=\"vf-text--body vf-text-body--5\">Jendrusch M <em>et al. <\/em>(2021). <a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.10.11.463937v1\">AlphaDesign: A de novo protein design framework based on AlphaFold<\/a>. <em>bioRxiv, <\/em>12 October 2021. DOI: 10.1101\/2021.10.11.463937<\/p>\n\n<\/div>\n<\/div>\n<\/div>\n\n\n<style>\n    <\/style>\n\n<section id=\"wp-block-1\">\n  <div class=\"vf-card-container  | vf-u-fullbleed  \n  | vf-u-background-color-ui--grey--light \">\n          <div class=\"vf-section-header | vf-u-margin__bottom--600\">\n        <h2 class=\"vf-section-header__heading\" >\n            <\/h2>\n              <\/div>\n      \n\n<div class=\"embl-grid\"><div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<h3 class=\"wp-block-heading\"><a href=\"https:\/\/www.embl.org\/about\/info\/annual-report\/\">Back to Annual report<\/a><\/h3>\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n  <img decoding=\"async\" width=\"1024\" height=\"612\" src=\"https:\/\/www.embl.org\/about\/info\/annual-report\/wp-content\/uploads\/2022\/02\/Technopolis-scaled-1-1024x612.jpeg\" class=\"vf-card__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/about\/info\/annual-report\/wp-content\/uploads\/2022\/02\/Technopolis-scaled-1-1024x612.jpeg 1024w, https:\/\/www.embl.org\/about\/info\/annual-report\/wp-content\/uploads\/2022\/02\/Technopolis-scaled-1-300x179.jpeg 300w, https:\/\/www.embl.org\/about\/info\/annual-report\/wp-content\/uploads\/2022\/02\/Technopolis-scaled-1-768x459.jpeg 768w, https:\/\/www.embl.org\/about\/info\/annual-report\/wp-content\/uploads\/2022\/02\/Technopolis-scaled-1-1536x918.jpeg 1536w, https:\/\/www.embl.org\/about\/info\/annual-report\/wp-content\/uploads\/2022\/02\/Technopolis-scaled-1-2048x1224.jpeg 2048w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/>\n  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n          <h3 class=\"vf-card__heading\">\n                  <a class=\"vf-card__link\" href=\"https:\/\/www.embl.org\/about\/info\/annual-report\/ar2021\/making-a-difference\" target=\"\">\n        \n        Next Story\n                  <svg aria-hidden=\"true\" class=\"vf-card__heading__icon | vf-icon vf-icon-arrow--inline-end\" width=\"1em\" height=\"1em\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\n            <path d=\"M0 12c0 6.627 5.373 12 12 12s12-5.373 12-12S18.627 0 12 0C5.376.008.008 5.376 0 12zm13.707-5.209l4.5 4.5a1 1 0 010 1.414l-4.5 4.5a1 1 0 01-1.414-1.414l2.366-2.367a.25.25 0 00-.177-.424H6a1 1 0 010-2h8.482a.25.25 0 00.177-.427l-2.366-2.368a1 1 0 011.414-1.414z\" fill=\"currentColor\" fill-rule=\"nonzero\"><\/path>\n          <\/svg>\n        <\/a>\n              <\/h3>\n    \n          <p class=\"vf-card__subheading\">Making a difference<\/p>\n    \n          <p class=\"vf-card__text\">External reviews illustrate the impact of EMBL services.<\/p>\n      <\/div>\n<\/article>\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n      <img decoding=\"async\" src=\"https:\/\/www.embl.org\/about\/info\/annual-report\/wp-content\/uploads\/2022\/06\/AR2021_PDF_mock-up_AdobeStock_182004081.jpg\" class=\"vf-card__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\">\n  \n  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n          <h3 class=\"vf-card__heading\">\n                  <a class=\"vf-card__link\" href=\"https:\/\/www.embl.org\/documents\/document\/annual-report-2021\/\" target=\"_blank\">\n        \n        Download the annual report summary \n                  <svg aria-hidden=\"true\" class=\"vf-card__heading__icon | vf-icon vf-icon-arrow--inline-end\" width=\"1em\" height=\"1em\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\n            <path d=\"M0 12c0 6.627 5.373 12 12 12s12-5.373 12-12S18.627 0 12 0C5.376.008.008 5.376 0 12zm13.707-5.209l4.5 4.5a1 1 0 010 1.414l-4.5 4.5a1 1 0 01-1.414-1.414l2.366-2.367a.25.25 0 00-.177-.424H6a1 1 0 010-2h8.482a.25.25 0 00.177-.427l-2.366-2.368a1 1 0 011.414-1.414z\" fill=\"currentColor\" fill-rule=\"nonzero\"><\/path>\n          <\/svg>\n        <\/a>\n              <\/h3>\n    \n    \n          <p class=\"vf-card__text\">A snapshot of EMBL 2021 facts and figures<\/p>\n      <\/div>\n<\/article>\n\n<\/div>\n<\/div>\n<\/div>\n\n\n        <\/div>\n<\/section>","protected":false},"excerpt":{"rendered":"","protected":false},"author":6,"featured_media":0,"parent":38,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"vf_template_subpage.php","meta":{"_acf_changed":false,"footnotes":""},"embl_taxonomy":[],"class_list":["post-896","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/about\/info\/annual-report\/wp-json\/wp\/v2\/pages\/896","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/about\/info\/annual-report\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.embl.org\/about\/info\/annual-report\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.embl.org\/about\/info\/annual-report\/wp-json\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/www.embl.org\/about\/info\/annual-report\/wp-json\/wp\/v2\/comments?post=896"}],"version-history":[{"count":48,"href":"https:\/\/www.embl.org\/about\/info\/annual-report\/wp-json\/wp\/v2\/pages\/896\/revisions"}],"predecessor-version":[{"id":3864,"href":"https:\/\/www.embl.org\/about\/info\/annual-report\/wp-json\/wp\/v2\/pages\/896\/revisions\/3864"}],"up":[{"embeddable":true,"href":"https:\/\/www.embl.org\/about\/info\/annual-report\/wp-json\/wp\/v2\/pages\/38"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/about\/info\/annual-report\/wp-json\/wp\/v2\/media?parent=896"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.embl.org\/about\/info\/annual-report\/wp-json\/wp\/v2\/embl_taxonomy?post=896"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}