{"id":985,"date":"2024-11-05T13:55:06","date_gmt":"2024-11-05T13:55:06","guid":{"rendered":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/?p=985"},"modified":"2024-12-10T14:53:02","modified_gmt":"2024-12-10T14:53:02","slug":"predicting-protein-structure-with-alphafold","status":"publish","type":"post","link":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/2024\/11\/05\/predicting-protein-structure-with-alphafold\/","title":{"rendered":"Predicting protein structures and building Legos"},"content":{"rendered":"

We welcome back guest blogger, Manya Bhargava<\/strong><\/a>, to explain this year’s Chemistry Nobel Prize, awarded to David Baker, Demis Hassabis and John Jumper, for the development of AlphaFold<\/strong>! Developed by Google DeepMind and EMBL-EBI, AlphaFold is an AI system that predicts protein structures.<\/p>\n

Imagine you\u2019ve just bought a new Lego set. You\u2019re super excited to get started. You have the pieces arranged, and all you need are the instructions to tell you how to fit them together. But someone seems to have played an awful prank on you. Instead of instructions in the box, you find a long list of clues about how the blocks need to fit together. Blue blocks can only connect to yellow ones, flat bricks can only be on the top\u2026 and so on. You know what the final model should look like, but this sure makes it much harder to build!<\/p>\n

<\/p>\n

\"Lego
Lego blocks. Image credit: Flickr, Tim Stahmer<\/figcaption><\/figure>\n

Much like Lego, proteins are made up of building blocks which all fit together in a very specific way to form the right structure. Scientists also have a list of clues as to how the blocks fit together. These are the physical forces underpinning how they interact with each other. For decades we\u2019ve been trying to figure out the \u2018instructions\u2019, so that we can take the building blocks of any protein and predict what the resulting structure would be. We call this the Protein Folding Problem<\/a>.<\/p>\n

The protein folding problem (PFP)<\/h2>\n

Proteins play a critical role in our bodies. They form antibodies to protect against disease and enzymes which speed up vital biological reactions. The function of a certain protein depends on its unique composition and shape.
\nSmaller \u2018blocks\u2019, called amino acids, link together by peptide bonds forming a polypeptide chain. This chain folds into a specific shape, called the native structure, which depends on the properties of the amino acids. There are 20 different types of amino acids, and each chain will have a different combination of these to form a unique protein.<\/p>\n

\"Protein
Protein folding process: from amino acids sequence to protein structure. Image credit: Manya Bhargava<\/figcaption><\/figure>\n

The ability to predict the shape of a folded protein from its amino acid sequence is an incredibly powerful tool. Applications include designing new drugs to target protein-related diseases like Alzheimer\u2019s and Parkinson\u2019s. This is, however, a very difficult task for classical computers. The nature of each amino acid, along with their interactions with each other and their environment, must be considered to find the protein\u2019s native structure, which leads to immensely complex calculations.<\/p>\n

AlphaFold<\/h2>\n

Recently, researchers turned to machine learning to solve the PFP by training AI to predict structures using a huge database of known protein shapes. This led to the release of AlphaFold<\/a> in 2021 (amongst similar technologies) which finds patterns between similar protein sequences. AlphaFold\u2019s success was groundbreaking. Making possible to map the structure of 98.5% of proteins in the human body when given the amino acid sequence.<\/p>\n

\"Two
Two examples of protein targets in the free modelling category. AlphaFold predicts highly accurate protein structures measured against experimental result. Image credit: Deep Mind.<\/figcaption><\/figure>\n

However, there are still challenges in the art of protein folding prediction. AlphaFold<\/a> is trained on a database of known proteins. Some of its success depends on the knowledge of these training structures, and not an understanding of the underlying physics behind folding. It\u2019s like memorising loads of Lego models and copying parts of their structures which use the same bricks that you have, rather than using the list of rules you\u2019ve been given.<\/p>\n

This method could lead to issues in predicting dynamic proteins which change shape to perform their functions, dealing with mutated (often disease-causing) proteins, and inaccuracies in those which don\u2019t have close relatives in the database \u2013 like proteins which may be designed for new drugs. Although AlphaFold was a revolutionary step forward, there is space for other techniques to fill in the gaps.<\/p>\n","protected":false},"excerpt":{"rendered":"

We welcome back guest blogger, Manya Bhargava, to explain this year’s Chemistry Nobel Prize, awarded to David Baker, Demis Hassabis and John Jumper, for the development of AlphaFold! Developed by Google DeepMind and EMBL-EBI, AlphaFold is an AI system that predicts protein structures. Imagine you\u2019ve just bought a new Lego set. You\u2019re super excited to […]<\/p>\n","protected":false},"author":1794,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[81490,48173],"tags":[81491,81492],"class_list":["post-985","post","type-post","status-publish","format-standard","hentry","category-quantum","category-uncategorised","tag-alphafold","tag-protein-structure"],"yoast_head":"\npredicting protein structure with alphafold<\/title>\n<meta name=\"description\" content=\"An AI method, awarded the Chemistry Nobel prize, responsible for predicting protein structure with alphafold\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/2024\/11\/05\/predicting-protein-structure-with-alphafold\/\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"predicting protein structure with alphafold\" \/>\n<meta property=\"og:description\" content=\"An AI method, awarded the Chemistry Nobel prize, responsible for predicting protein structure with alphafold\" \/>\n<meta property=\"og:url\" content=\"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/2024\/11\/05\/predicting-protein-structure-with-alphafold\/\" \/>\n<meta property=\"og:site_name\" content=\"Institute for Molecular Science and Engineering\" \/>\n<meta property=\"article:published_time\" content=\"2024-11-05T13:55:06+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2024-12-10T14:53:02+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/files\/2024\/10\/Flickr.-Tim-Stahmer.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"799\" \/>\n\t<meta property=\"og:image:height\" content=\"533\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"author\" content=\"Elena Corujo Simon\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Elena Corujo Simon\" \/>\n\t<meta name=\"twitter:label2\" content=\"Estimated reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"4 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/2024\\\/11\\\/05\\\/predicting-protein-structure-with-alphafold\\\/#article\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/2024\\\/11\\\/05\\\/predicting-protein-structure-with-alphafold\\\/\"},\"author\":{\"name\":\"Elena Corujo Simon\",\"@id\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/#\\\/schema\\\/person\\\/70073378a832624eead50b96ea3aa43b\"},\"headline\":\"Predicting protein structures and building Legos\",\"datePublished\":\"2024-11-05T13:55:06+00:00\",\"dateModified\":\"2024-12-10T14:53:02+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/2024\\\/11\\\/05\\\/predicting-protein-structure-with-alphafold\\\/\"},\"wordCount\":688,\"image\":{\"@id\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/2024\\\/11\\\/05\\\/predicting-protein-structure-with-alphafold\\\/#primaryimage\"},\"thumbnailUrl\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/files\\\/2024\\\/10\\\/Flickr.-Tim-Stahmer.jpg\",\"keywords\":[\"alphafold\",\"protein structure\"],\"articleSection\":[\"Quantum\"],\"inLanguage\":\"en-GB\"},{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/2024\\\/11\\\/05\\\/predicting-protein-structure-with-alphafold\\\/\",\"url\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/2024\\\/11\\\/05\\\/predicting-protein-structure-with-alphafold\\\/\",\"name\":\"predicting protein structure with alphafold\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/2024\\\/11\\\/05\\\/predicting-protein-structure-with-alphafold\\\/#primaryimage\"},\"image\":{\"@id\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/2024\\\/11\\\/05\\\/predicting-protein-structure-with-alphafold\\\/#primaryimage\"},\"thumbnailUrl\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/files\\\/2024\\\/10\\\/Flickr.-Tim-Stahmer.jpg\",\"datePublished\":\"2024-11-05T13:55:06+00:00\",\"dateModified\":\"2024-12-10T14:53:02+00:00\",\"author\":{\"@id\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/#\\\/schema\\\/person\\\/70073378a832624eead50b96ea3aa43b\"},\"description\":\"An AI method, awarded the Chemistry Nobel prize, responsible for predicting protein structure with alphafold\",\"breadcrumb\":{\"@id\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/2024\\\/11\\\/05\\\/predicting-protein-structure-with-alphafold\\\/#breadcrumb\"},\"inLanguage\":\"en-GB\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/2024\\\/11\\\/05\\\/predicting-protein-structure-with-alphafold\\\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"en-GB\",\"@id\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/2024\\\/11\\\/05\\\/predicting-protein-structure-with-alphafold\\\/#primaryimage\",\"url\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/files\\\/2024\\\/10\\\/Flickr.-Tim-Stahmer.jpg\",\"contentUrl\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/files\\\/2024\\\/10\\\/Flickr.-Tim-Stahmer.jpg\",\"width\":799,\"height\":533,\"caption\":\"Lego blocks. Image credit: Flickr, Tim Stahmer\"},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/2024\\\/11\\\/05\\\/predicting-protein-structure-with-alphafold\\\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Predicting protein structures and building Legos\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/#website\",\"url\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/\",\"name\":\"Institute for Molecular Science and Engineering\",\"description\":\"Bringing to life the power of molecules\",\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/?s={search_term_string}\"},\"query-input\":{\"@type\":\"PropertyValueSpecification\",\"valueRequired\":true,\"valueName\":\"search_term_string\"}}],\"inLanguage\":\"en-GB\"},{\"@type\":\"Person\",\"@id\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/#\\\/schema\\\/person\\\/70073378a832624eead50b96ea3aa43b\",\"name\":\"Elena Corujo Simon\",\"image\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-GB\",\"@id\":\"https:\\\/\\\/secure.gravatar.com\\\/avatar\\\/97b59324a02a5f560e5c815f95441b544c6fd8ad443858124860e4173bd65d11?s=96&d=mm&r=g\",\"url\":\"https:\\\/\\\/secure.gravatar.com\\\/avatar\\\/97b59324a02a5f560e5c815f95441b544c6fd8ad443858124860e4173bd65d11?s=96&d=mm&r=g\",\"contentUrl\":\"https:\\\/\\\/secure.gravatar.com\\\/avatar\\\/97b59324a02a5f560e5c815f95441b544c6fd8ad443858124860e4173bd65d11?s=96&d=mm&r=g\",\"caption\":\"Elena Corujo Simon\"},\"url\":\"https:\\\/\\\/blogs.imperial.ac.uk\\\/molecular-science-engineering\\\/author\\\/ecorujos\\\/\"}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"predicting protein structure with alphafold","description":"An AI method, awarded the Chemistry Nobel prize, responsible for predicting protein structure with alphafold","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/2024\/11\/05\/predicting-protein-structure-with-alphafold\/","og_locale":"en_GB","og_type":"article","og_title":"predicting protein structure with alphafold","og_description":"An AI method, awarded the Chemistry Nobel prize, responsible for predicting protein structure with alphafold","og_url":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/2024\/11\/05\/predicting-protein-structure-with-alphafold\/","og_site_name":"Institute for Molecular Science and Engineering","article_published_time":"2024-11-05T13:55:06+00:00","article_modified_time":"2024-12-10T14:53:02+00:00","og_image":[{"width":799,"height":533,"url":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/files\/2024\/10\/Flickr.-Tim-Stahmer.jpg","type":"image\/jpeg"}],"author":"Elena Corujo Simon","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Elena Corujo Simon","Estimated reading time":"4 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/2024\/11\/05\/predicting-protein-structure-with-alphafold\/#article","isPartOf":{"@id":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/2024\/11\/05\/predicting-protein-structure-with-alphafold\/"},"author":{"name":"Elena Corujo Simon","@id":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/#\/schema\/person\/70073378a832624eead50b96ea3aa43b"},"headline":"Predicting protein structures and building Legos","datePublished":"2024-11-05T13:55:06+00:00","dateModified":"2024-12-10T14:53:02+00:00","mainEntityOfPage":{"@id":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/2024\/11\/05\/predicting-protein-structure-with-alphafold\/"},"wordCount":688,"image":{"@id":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/2024\/11\/05\/predicting-protein-structure-with-alphafold\/#primaryimage"},"thumbnailUrl":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/files\/2024\/10\/Flickr.-Tim-Stahmer.jpg","keywords":["alphafold","protein structure"],"articleSection":["Quantum"],"inLanguage":"en-GB"},{"@type":"WebPage","@id":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/2024\/11\/05\/predicting-protein-structure-with-alphafold\/","url":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/2024\/11\/05\/predicting-protein-structure-with-alphafold\/","name":"predicting protein structure with alphafold","isPartOf":{"@id":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/#website"},"primaryImageOfPage":{"@id":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/2024\/11\/05\/predicting-protein-structure-with-alphafold\/#primaryimage"},"image":{"@id":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/2024\/11\/05\/predicting-protein-structure-with-alphafold\/#primaryimage"},"thumbnailUrl":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/files\/2024\/10\/Flickr.-Tim-Stahmer.jpg","datePublished":"2024-11-05T13:55:06+00:00","dateModified":"2024-12-10T14:53:02+00:00","author":{"@id":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/#\/schema\/person\/70073378a832624eead50b96ea3aa43b"},"description":"An AI method, awarded the Chemistry Nobel prize, responsible for predicting protein structure with alphafold","breadcrumb":{"@id":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/2024\/11\/05\/predicting-protein-structure-with-alphafold\/#breadcrumb"},"inLanguage":"en-GB","potentialAction":[{"@type":"ReadAction","target":["https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/2024\/11\/05\/predicting-protein-structure-with-alphafold\/"]}]},{"@type":"ImageObject","inLanguage":"en-GB","@id":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/2024\/11\/05\/predicting-protein-structure-with-alphafold\/#primaryimage","url":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/files\/2024\/10\/Flickr.-Tim-Stahmer.jpg","contentUrl":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/files\/2024\/10\/Flickr.-Tim-Stahmer.jpg","width":799,"height":533,"caption":"Lego blocks. Image credit: Flickr, Tim Stahmer"},{"@type":"BreadcrumbList","@id":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/2024\/11\/05\/predicting-protein-structure-with-alphafold\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/"},{"@type":"ListItem","position":2,"name":"Predicting protein structures and building Legos"}]},{"@type":"WebSite","@id":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/#website","url":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/","name":"Institute for Molecular Science and Engineering","description":"Bringing to life the power of molecules","potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-GB"},{"@type":"Person","@id":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/#\/schema\/person\/70073378a832624eead50b96ea3aa43b","name":"Elena Corujo Simon","image":{"@type":"ImageObject","inLanguage":"en-GB","@id":"https:\/\/secure.gravatar.com\/avatar\/97b59324a02a5f560e5c815f95441b544c6fd8ad443858124860e4173bd65d11?s=96&d=mm&r=g","url":"https:\/\/secure.gravatar.com\/avatar\/97b59324a02a5f560e5c815f95441b544c6fd8ad443858124860e4173bd65d11?s=96&d=mm&r=g","contentUrl":"https:\/\/secure.gravatar.com\/avatar\/97b59324a02a5f560e5c815f95441b544c6fd8ad443858124860e4173bd65d11?s=96&d=mm&r=g","caption":"Elena Corujo Simon"},"url":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/author\/ecorujos\/"}]}},"_links":{"self":[{"href":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/wp-json\/wp\/v2\/posts\/985","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/wp-json\/wp\/v2\/users\/1794"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/wp-json\/wp\/v2\/comments?post=985"}],"version-history":[{"count":11,"href":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/wp-json\/wp\/v2\/posts\/985\/revisions"}],"predecessor-version":[{"id":1018,"href":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/wp-json\/wp\/v2\/posts\/985\/revisions\/1018"}],"wp:attachment":[{"href":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/wp-json\/wp\/v2\/media?parent=985"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/wp-json\/wp\/v2\/categories?post=985"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.imperial.ac.uk\/molecular-science-engineering\/wp-json\/wp\/v2\/tags?post=985"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}