{"id":464919,"date":"2022-06-18T13:54:44","date_gmt":"2022-06-18T10:54:44","guid":{"rendered":"https:\/\/en.buradabiliyorum.com\/a-celebrated-ai-has-learned-a-new-trick-how-to-do-chemistry\/"},"modified":"2022-06-18T13:54:44","modified_gmt":"2022-06-18T10:54:44","slug":"a-celebrated-ai-has-learned-a-new-trick-how-to-do-chemistry","status":"publish","type":"post","link":"https:\/\/buradabiliyorum.com\/en\/a-celebrated-ai-has-learned-a-new-trick-how-to-do-chemistry\/","title":{"rendered":"#A celebrated AI has learned a new trick: How to do\u00a0chemistry"},"content":{"rendered":"<div id=\"ez-toc-container\" class=\"ez-toc-v2_0_85 counter-hierarchy ez-toc-counter ez-toc-custom ez-toc-container-direction\">\n<p class=\"ez-toc-title\" style=\"cursor:inherit\">Table of Contents<\/p>\n<label for=\"ez-toc-cssicon-toggle-item-6a3848e6556b6\" class=\"ez-toc-cssicon-toggle-label\"><span class=\"\"><span class=\"eztoc-hide\" style=\"display:none;\">Toggle<\/span><span class=\"ez-toc-icon-toggle-span\"><svg style=\"fill: #dd3333;color:#dd3333\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" class=\"list-377408\" width=\"20px\" height=\"20px\" viewBox=\"0 0 24 24\" fill=\"none\"><path d=\"M6 6H4v2h2V6zm14 0H8v2h12V6zM4 11h2v2H4v-2zm16 0H8v2h12v-2zM4 16h2v2H4v-2zm16 0H8v2h12v-2z\" fill=\"currentColor\"><\/path><\/svg><svg style=\"fill: #dd3333;color:#dd3333\" class=\"arrow-unsorted-368013\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" width=\"10px\" height=\"10px\" viewBox=\"0 0 24 24\" version=\"1.2\" baseProfile=\"tiny\"><path d=\"M18.2 9.3l-6.2-6.3-6.2 6.3c-.2.2-.3.4-.3.7s.1.5.3.7c.2.2.4.3.7.3h11c.3 0 .5-.1.7-.3.2-.2.3-.5.3-.7s-.1-.5-.3-.7zM5.8 14.7l6.2 6.3 6.2-6.3c.2-.2.3-.5.3-.7s-.1-.5-.3-.7c-.2-.2-.4-.3-.7-.3h-11c-.3 0-.5.1-.7.3-.2.2-.3.5-.3.7s.1.5.3.7z\"\/><\/svg><\/span><\/span><\/label><input type=\"checkbox\"  id=\"ez-toc-cssicon-toggle-item-6a3848e6556b6\" checked aria-label=\"Toggle\" \/><nav><ul class='ez-toc-list ez-toc-list-level-1 ' ><li class='ez-toc-page-1 ez-toc-heading-level-1'><a class=\"ez-toc-link ez-toc-heading-1\" href=\"https:\/\/buradabiliyorum.com\/en\/a-celebrated-ai-has-learned-a-new-trick-how-to-do-chemistry\/#%E2%80%9CA_celebrated_AI_has_learned_a_new_trick_How_to_do_chemistry%E2%80%9D\" >&#8220;A celebrated AI has learned a new trick: How to do\u00a0chemistry&#8221;<\/a><ul class='ez-toc-list-level-2' ><li class='ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-2\" href=\"https:\/\/buradabiliyorum.com\/en\/a-celebrated-ai-has-learned-a-new-trick-how-to-do-chemistry\/#Protein_folding\" >Protein folding<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-3\" href=\"https:\/\/buradabiliyorum.com\/en\/a-celebrated-ai-has-learned-a-new-trick-how-to-do-chemistry\/#Greetings_humanoids\" >Greetings, humanoids<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-4\" href=\"https:\/\/buradabiliyorum.com\/en\/a-celebrated-ai-has-learned-a-new-trick-how-to-do-chemistry\/#AlphaFold\" >AlphaFold<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-5\" href=\"https:\/\/buradabiliyorum.com\/en\/a-celebrated-ai-has-learned-a-new-trick-how-to-do-chemistry\/#Thinking_like_a_chemist\" >Thinking like a chemist<\/a><\/li><\/ul><\/li><\/ul><\/nav><\/div>\n<h1><span class=\"ez-toc-section\" id=\"%E2%80%9CA_celebrated_AI_has_learned_a_new_trick_How_to_do_chemistry%E2%80%9D\"><\/span>&#8220;A celebrated AI has learned a new trick: How to do\u00a0chemistry&#8221;<span class=\"ez-toc-section-end\"><\/span><\/h1>\n<div id=\"article-main-content\">\n                            Artificial intelligence has changed the way <a href=\"https:\/\/buradabiliyorum.com\/en\/category\/sciencee\/\" data-internallinksmanager029f6b8e52c=\"5\" title=\"Science\" target=\"_blank\" rel=\"noopener\">science<\/a> is done by allowing researchers to analyze the massive amounts of data modern scientific instruments generate. It can find a needle in a million haystacks of information and, using <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/www.techtarget.com\/searchenterpriseai\/definition\/deep-learning-deep-neural-network\">deep learning<\/a>, it can learn from the data itself. AI is accelerating advances in <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/doi.org\/10.1186\/s13073-021-00965-0\">gene hunting<\/a>, <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/doi.org\/10.1038\/s41591-020-01197-2\">medicine<\/a>, <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/news.mit.edu\/2021\/drug-discovery-binding-affinity-0315\">drug design<\/a> and <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/doi.org\/10.1038\/nature25978\">the creation of organic compounds<\/a>.<\/p>\n<p>Deep learning uses algorithms, often neural networks that are trained on large amounts of data, to extract information from new data. It is very different from traditional computing with its step-by-step instructions. Rather, it learns from data. Deep learning is far less transparent than traditional computer programming, leaving important questions \u2013 what has the system learned, what does it know?<\/p>\n<p>As a <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/scholar.google.ca\/citations?user=RpiSPiwAAAAJ&amp;hl=en\">chemistry professor<\/a> I like to design tests that have at least one difficult question that stretches the students\u2019 knowledge to establish whether they can combine different ideas and synthesize new ideas and concepts. We have devised such a question for the poster child of AI advocates, AlphaFold, which has solved the <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/doi.org\/10.1146%2Fannurev.biophys.37.092707.153558\">protein-folding problem<\/a>.<\/p>\n<h2><span class=\"ez-toc-section\" id=\"Protein_folding\"><\/span>Protein folding<span class=\"ez-toc-section-end\"><\/span><\/h2>\n<div class=\"inarticle-wrapper neural channel-cta hs-embed-tnw\">\n<div id=\"hs-embed-tnw\" class=\"channel-cta-wrapper\">\n<div class=\"channel-cta-img\"><img decoding=\"async\" src=\"https:\/\/s3.amazonaws.com\/uploads.tnw\/uploads\/neural-newsletter_header-1.gif\"\/><\/div>\n<p><noscript><img decoding=\"async\" src=\"https:\/\/thenextweb.com\/news\/src=\" https:=\"\"\/><\/noscript><\/p>\n<div class=\"channel-cta-input\">\n<h2 class=\"channel-cta-title\"><span class=\"ez-toc-section\" id=\"Greetings_humanoids\"><\/span>Greetings, humanoids<span class=\"ez-toc-section-end\"><\/span><\/h2>\n<p class=\"channel-cta-tagline\">Subscribe to our <a href=\"https:\/\/buradabiliyorum.com\/en\/category\/news\/\" data-internallinksmanager029f6b8e52c=\"2\" title=\"News\" target=\"_blank\" rel=\"noopener\">news<\/a>letter now for a weekly recap of our favorite AI stories in your inbox.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<p>Proteins are present in all living organisms. They provide the cells with structure, catalyze reactions, transport small molecules, digest food and do much more. They are made up of long chains of amino acids like beads on a string. But for a protein to do its job in the cell, it must twist and bend into a complex three-dimensional structure, a process called protein folding. Misfolded proteins can lead to disease.<\/p>\n<p>In his chemistry Nobel acceptance speech in 1972, <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/www.nobelprize.org\/prizes\/chemistry\/1972\/anfinsen\/biographical\/\">Christiaan Anfinsen<\/a> postulated that it should be possible to <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/directorsblog.nih.gov\/tag\/christian-anfinsen\/\">calculate the three-dimensional structure of a protein from the sequence of its building blocks<\/a>, the amino acids.<\/p>\n<p>Just as the order and spacing of the letters in this article give it sense and message, so the order of the amino acids determines the protein\u2019s identity and shape, which results in its function.<\/p>\n<figure class=\"align-center zoomable\"><a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/images.theconversation.com\/files\/462041\/original\/file-20220509-23-mkr8t2.png?ixlib=rb-1.1.0&amp;q=45&amp;auto=format&amp;w=1000&amp;fit=clip\"><img sizes=\"(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px\" alt=\"a graphic showing a thread-like line on the left and a coiled structure on the right\" class=\"js-lazy\" https:=\"\" srcset=\"https:\/\/images.theconversation.com\/files\/462041\/original\/file-20220509-23-mkr8t2.png?ixlib=rb-1.1.0&amp;q=45&amp;auto=format&amp;w=600&amp;h=266&amp;fit=crop&amp;dpr=1 600w, https:\/\/images.theconversation.com\/files\/462041\/original\/file-20220509-23-mkr8t2.png?ixlib=rb-1.1.0&amp;q=30&amp;auto=format&amp;w=600&amp;h=266&amp;fit=crop&amp;dpr=2 1200w, https:\/\/images.theconversation.com\/files\/462041\/original\/file-20220509-23-mkr8t2.png?ixlib=rb-1.1.0&amp;q=15&amp;auto=format&amp;w=600&amp;h=266&amp;fit=crop&amp;dpr=3 1800w, https:\/\/images.theconversation.com\/files\/462041\/original\/file-20220509-23-mkr8t2.png?ixlib=rb-1.1.0&amp;q=45&amp;auto=format&amp;w=754&amp;h=334&amp;fit=crop&amp;dpr=1 754w, https:\/\/images.theconversation.com\/files\/462041\/original\/file-20220509-23-mkr8t2.png?ixlib=rb-1.1.0&amp;q=30&amp;auto=format&amp;w=754&amp;h=334&amp;fit=crop&amp;dpr=2 1508w, https:\/\/images.theconversation.com\/files\/462041\/original\/file-20220509-23-mkr8t2.png?ixlib=rb-1.1.0&amp;q=15&amp;auto=format&amp;w=754&amp;h=334&amp;fit=crop&amp;dpr=3 2262w\"\/><noscript><img decoding=\"async\" src=\"https:\/\/images.theconversation.com\/files\/462041\/original\/file-20220509-23-mkr8t2.png?ixlib=rb-1.1.0&amp;q=45&amp;auto=format&amp;w=754&amp;fit=clip\" alt=\"a graphic showing a thread-like line on the left and a coiled structure on the right\" class=\"\" srcset=\"https:\/\/images.theconversation.com\/files\/462041\/original\/file-20220509-23-mkr8t2.png?ixlib=rb-1.1.0&amp;q=45&amp;auto=format&amp;w=600&amp;h=266&amp;fit=crop&amp;dpr=1 600w, https:\/\/images.theconversation.com\/files\/462041\/original\/file-20220509-23-mkr8t2.png?ixlib=rb-1.1.0&amp;q=30&amp;auto=format&amp;w=600&amp;h=266&amp;fit=crop&amp;dpr=2 1200w, https:\/\/images.theconversation.com\/files\/462041\/original\/file-20220509-23-mkr8t2.png?ixlib=rb-1.1.0&amp;q=15&amp;auto=format&amp;w=600&amp;h=266&amp;fit=crop&amp;dpr=3 1800w, https:\/\/images.theconversation.com\/files\/462041\/original\/file-20220509-23-mkr8t2.png?ixlib=rb-1.1.0&amp;q=45&amp;auto=format&amp;w=754&amp;h=334&amp;fit=crop&amp;dpr=1 754w, https:\/\/images.theconversation.com\/files\/462041\/original\/file-20220509-23-mkr8t2.png?ixlib=rb-1.1.0&amp;q=30&amp;auto=format&amp;w=754&amp;h=334&amp;fit=crop&amp;dpr=2 1508w, https:\/\/images.theconversation.com\/files\/462041\/original\/file-20220509-23-mkr8t2.png?ixlib=rb-1.1.0&amp;q=15&amp;auto=format&amp;w=754&amp;h=334&amp;fit=crop&amp;dpr=3 2262w\"\/><\/noscript><\/a><figcaption><span class=\"caption\">Within milliseconds of the exit of an amino acid chain (left) from the ribosome, it is folded into the lowest-energy 3D shape (right), which is required for the protein\u2019s function.<\/span><br \/><span class=\"attribution\"><span class=\"source\">Marc Zimmer<\/span>, <a rel=\"nofollow noopener\" target=\"_blank\" class=\"license\" href=\"https:\/\/creativecommons.org\/licenses\/by-nd\/4.0\/\">CC BY-ND<\/a><\/span><\/figcaption><\/figure>\n<p>Because of the inherent flexibility of the amino acid building blocks, a typical protein can adopt an estimated <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/web.archive.org\/web\/20110523080407\/http:\/www-miller.ch.cam.ac.uk\/levinthal\/levinthal.html\">10 to the power of 300 different forms<\/a>. This is a massive number, more than the <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/educationblog.oup.com\/secondary\/maths\/numbers-of-atoms-in-the-universe\">number of atoms in the universe<\/a>. Yet within a millisecond every protein in an organism will fold into its very own specific shape \u2013 the lowest-energy arrangement of all the chemical bonds that make up the protein. Change just one amino acid in the hundreds of amino acids typically found in a protein and it may misfold and no longer work.<\/p>\n<h2><span class=\"ez-toc-section\" id=\"AlphaFold\"><\/span>AlphaFold<span class=\"ez-toc-section-end\"><\/span><\/h2>\n<p>For 50 years computer scientists have tried to solve the protein-folding problem \u2013 with little success. Then in 2016 <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/www.deepmind.com\/\">DeepMind<\/a>, an AI subsidiary of Google parent Alphabet, initiated its <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/www.deepmind.com\/blog\/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology\">AlphaFold<\/a> program. It used the <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/www.rcsb.org\/\">protein databank<\/a> as its training set, which contains the experimentally determined structures of over 150,000 proteins.<\/p>\n<p>In less than five years AlphaFold had <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/www.deepmind.com\/blog\/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology\">the protein-folding problem beat<\/a> \u2013 at least the most useful part of it, namely, determining the protein structure from its amino acid sequence. AlphaFold does not explain how the proteins fold so quickly and accurately. It was a major win for AI, because it not only accrued huge scientific prestige, it also was a major scientific advance that could affect everyone\u2019s lives.<\/p>\n<p>Today, thanks to programs like <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/www.deepmind.com\/blog\/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology\">AlphaFold2<\/a> and <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/www.ipd.uw.edu\/2021\/07\/rosettafold-accurate-protein-structure-prediction-accessible-to-all\/\">RoseTTAFold<\/a>, researchers like me can determine the three-dimensional structure of proteins from the sequence of amino acids that make up the protein \u2013 at no cost \u2013 in an hour or two. Before AlphaFold2 we had to crystallize the proteins and solve the structures using <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/doi.org\/10.1136%2Fmp.53.1.8\">X-ray crystallography<\/a>, a process that took months and cost tens of thousands of dollars per structure.<\/p>\n<p>We now also have access to the <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/alphafold.ebi.ac.uk\/\">AlphaFold Protein Structure Database<\/a>, where Deepmind has deposited the 3D structures of nearly all the proteins found in humans, mice and more than 20 other species. To date they it has solved more than a million structures and plan to add another 100 million structures this year alone. Knowledge of proteins has skyrocketed. The structure of half of all known proteins is likely to be documented by the end of 2022, among them many new unique structures associated with new useful functions.<\/p>\n<h2><span class=\"ez-toc-section\" id=\"Thinking_like_a_chemist\"><\/span>Thinking like a chemist<span class=\"ez-toc-section-end\"><\/span><\/h2>\n<p>AlphaFold2 was not designed to predict how proteins would interact with one another, yet it has been able to model how individual proteins combine to <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/www.nature.com\/articles\/d41586-022-00997-5\">form large complex units composed of multiple proteins<\/a>. We had a challenging question for AlphaFold \u2013 had its structural training set taught it some chemistry? Could it tell whether amino acids would react with one another \u2013 a rare yet important occurrence?<\/p>\n<p>I am a computational chemist interested in <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/theconversation.com\/fluorescent-proteins-light-up-science-by-making-the-invisible-visible-39272\">fluorescent proteins<\/a>. These are proteins found in hundreds of marine organisms like jellyfish and coral. Their glow can be used <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/theconversation.com\/from-crispr-to-glowing-proteins-to-optogenetics-scientists-most-powerful-technologies-have-been-borrowed-from-nature-164459\">to illuminate<\/a> and <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/global.oup.com\/academic\/product\/illuminating-disease-9780199362813?cc=us&amp;lang=en&amp;\">study diseases<\/a>.<\/p>\n<figure class=\"align-center zoomable\"><a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/images.theconversation.com\/files\/468852\/original\/file-20220614-12-84y9j5.jpg?ixlib=rb-1.1.0&amp;q=45&amp;auto=format&amp;w=1000&amp;fit=clip\"><img sizes=\"(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px\" alt=\"two multicolored blobs with bright lines inside them against a black background\" class=\"js-lazy\" https:=\"\" srcset=\"https:\/\/images.theconversation.com\/files\/468852\/original\/file-20220614-12-84y9j5.jpg?ixlib=rb-1.1.0&amp;q=45&amp;auto=format&amp;w=600&amp;h=302&amp;fit=crop&amp;dpr=1 600w, https:\/\/images.theconversation.com\/files\/468852\/original\/file-20220614-12-84y9j5.jpg?ixlib=rb-1.1.0&amp;q=30&amp;auto=format&amp;w=600&amp;h=302&amp;fit=crop&amp;dpr=2 1200w, https:\/\/images.theconversation.com\/files\/468852\/original\/file-20220614-12-84y9j5.jpg?ixlib=rb-1.1.0&amp;q=15&amp;auto=format&amp;w=600&amp;h=302&amp;fit=crop&amp;dpr=3 1800w, https:\/\/images.theconversation.com\/files\/468852\/original\/file-20220614-12-84y9j5.jpg?ixlib=rb-1.1.0&amp;q=45&amp;auto=format&amp;w=754&amp;h=379&amp;fit=crop&amp;dpr=1 754w, https:\/\/images.theconversation.com\/files\/468852\/original\/file-20220614-12-84y9j5.jpg?ixlib=rb-1.1.0&amp;q=30&amp;auto=format&amp;w=754&amp;h=379&amp;fit=crop&amp;dpr=2 1508w, https:\/\/images.theconversation.com\/files\/468852\/original\/file-20220614-12-84y9j5.jpg?ixlib=rb-1.1.0&amp;q=15&amp;auto=format&amp;w=754&amp;h=379&amp;fit=crop&amp;dpr=3 2262w\"\/><noscript><img decoding=\"async\" src=\"https:\/\/images.theconversation.com\/files\/468852\/original\/file-20220614-12-84y9j5.jpg?ixlib=rb-1.1.0&amp;q=45&amp;auto=format&amp;w=754&amp;fit=clip\" alt=\"two multicolored blobs with bright lines inside them against a black background\" class=\"\" srcset=\"https:\/\/images.theconversation.com\/files\/468852\/original\/file-20220614-12-84y9j5.jpg?ixlib=rb-1.1.0&amp;q=45&amp;auto=format&amp;w=600&amp;h=302&amp;fit=crop&amp;dpr=1 600w, https:\/\/images.theconversation.com\/files\/468852\/original\/file-20220614-12-84y9j5.jpg?ixlib=rb-1.1.0&amp;q=30&amp;auto=format&amp;w=600&amp;h=302&amp;fit=crop&amp;dpr=2 1200w, https:\/\/images.theconversation.com\/files\/468852\/original\/file-20220614-12-84y9j5.jpg?ixlib=rb-1.1.0&amp;q=15&amp;auto=format&amp;w=600&amp;h=302&amp;fit=crop&amp;dpr=3 1800w, https:\/\/images.theconversation.com\/files\/468852\/original\/file-20220614-12-84y9j5.jpg?ixlib=rb-1.1.0&amp;q=45&amp;auto=format&amp;w=754&amp;h=379&amp;fit=crop&amp;dpr=1 754w, https:\/\/images.theconversation.com\/files\/468852\/original\/file-20220614-12-84y9j5.jpg?ixlib=rb-1.1.0&amp;q=30&amp;auto=format&amp;w=754&amp;h=379&amp;fit=crop&amp;dpr=2 1508w, https:\/\/images.theconversation.com\/files\/468852\/original\/file-20220614-12-84y9j5.jpg?ixlib=rb-1.1.0&amp;q=15&amp;auto=format&amp;w=754&amp;h=379&amp;fit=crop&amp;dpr=3 2262w\"\/><\/noscript><\/a><figcaption><span class=\"caption\">Neurons expressing fluorescent proteins reveal the brain structures of two fruit fly larvae.<\/span><br \/><span class=\"attribution\"><a rel=\"nofollow noopener\" target=\"_blank\" class=\"source\" href=\"https:\/\/images.nigms.nih.gov\/pages\/DetailPage.aspx?imageid2=6808\">Wen Lu and Vladimir I. Gelfand, Feinberg School of Medicine, Northwestern University<\/a><\/span><\/figcaption><\/figure>\n<p>There are 578 fluorescent proteins in the <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/www.rcsb.org\/search?request=%7B%22query%22%3A%7B%22type%22%3A%22group%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22group%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22group%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22terminal%22%2C%22service%22%3A%22text%22%2C%22parameters%22%3A%7B%22attribute%22%3A%22struct_keywords.pdbx_keywords%22%2C%22operator%22%3A%22contains_phrase%22%2C%22value%22%3A%22FLUORESCENT%20PROTEIN%22%7D%7D%5D%2C%22logical_operator%22%3A%22and%22%7D%5D%2C%22logical_operator%22%3A%22and%22%2C%22label%22%3A%22text%22%7D%5D%2C%22logical_operator%22%3A%22and%22%7D%2C%22return_type%22%3A%22entry%22%2C%22request_options%22%3A%7B%22paginate%22%3A%7B%22start%22%3A0%2C%22rows%22%3A25%7D%2C%22scoring_strategy%22%3A%22combined%22%2C%22sort%22%3A%5B%7B%22sort_by%22%3A%22score%22%2C%22direction%22%3A%22desc%22%7D%5D%7D%2C%22request_info%22%3A%7B%22query_id%22%3A%223e70236cf383b26f27688c5c79c6eb2b%22%7D%7D\">protein databank<\/a>, of which 10 are \u201cbroken\u201d and don\u2019t fluoresce. Proteins rarely attack themselves, a process called autocatalytic posttranslation modification, and it is very difficult to predict which proteins will react with themselves and which ones won\u2019t.<\/p>\n<p>Only a chemist with a significant amount of fluorescent protein knowledge would be able to use the amino acid sequence to find the fluorescent proteins that have the right amino acid sequence to undergo the chemical transformations required to make them fluorescent. When we presented AlphaFold2 with the sequences of 44 fluorescent proteins that are not in the protein databank, <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0267560\">it folded the fixed fluorescent proteins differently from the broken ones<\/a>.<\/p>\n<figure class=\"align-center zoomable\"><a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/images.theconversation.com\/files\/462050\/original\/file-20220509-12-fxhj9p.png?ixlib=rb-1.1.0&amp;q=45&amp;auto=format&amp;w=1000&amp;fit=clip\"><img sizes=\"(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px\" alt=\"a diagram showing a light bulb on the left and the stem only of a light bulb on the right\" class=\"js-lazy\" https:=\"\" srcset=\"https:\/\/images.theconversation.com\/files\/462050\/original\/file-20220509-12-fxhj9p.png?ixlib=rb-1.1.0&amp;q=45&amp;auto=format&amp;w=600&amp;h=333&amp;fit=crop&amp;dpr=1 600w, https:\/\/images.theconversation.com\/files\/462050\/original\/file-20220509-12-fxhj9p.png?ixlib=rb-1.1.0&amp;q=30&amp;auto=format&amp;w=600&amp;h=333&amp;fit=crop&amp;dpr=2 1200w, https:\/\/images.theconversation.com\/files\/462050\/original\/file-20220509-12-fxhj9p.png?ixlib=rb-1.1.0&amp;q=15&amp;auto=format&amp;w=600&amp;h=333&amp;fit=crop&amp;dpr=3 1800w, https:\/\/images.theconversation.com\/files\/462050\/original\/file-20220509-12-fxhj9p.png?ixlib=rb-1.1.0&amp;q=45&amp;auto=format&amp;w=754&amp;h=419&amp;fit=crop&amp;dpr=1 754w, https:\/\/images.theconversation.com\/files\/462050\/original\/file-20220509-12-fxhj9p.png?ixlib=rb-1.1.0&amp;q=30&amp;auto=format&amp;w=754&amp;h=419&amp;fit=crop&amp;dpr=2 1508w, https:\/\/images.theconversation.com\/files\/462050\/original\/file-20220509-12-fxhj9p.png?ixlib=rb-1.1.0&amp;q=15&amp;auto=format&amp;w=754&amp;h=419&amp;fit=crop&amp;dpr=3 2262w\"\/><noscript><img decoding=\"async\" src=\"https:\/\/images.theconversation.com\/files\/462050\/original\/file-20220509-12-fxhj9p.png?ixlib=rb-1.1.0&amp;q=45&amp;auto=format&amp;w=754&amp;fit=clip\" alt=\"a diagram showing a light bulb on the left and the stem only of a light bulb on the right\" class=\"\" srcset=\"https:\/\/images.theconversation.com\/files\/462050\/original\/file-20220509-12-fxhj9p.png?ixlib=rb-1.1.0&amp;q=45&amp;auto=format&amp;w=600&amp;h=333&amp;fit=crop&amp;dpr=1 600w, https:\/\/images.theconversation.com\/files\/462050\/original\/file-20220509-12-fxhj9p.png?ixlib=rb-1.1.0&amp;q=30&amp;auto=format&amp;w=600&amp;h=333&amp;fit=crop&amp;dpr=2 1200w, https:\/\/images.theconversation.com\/files\/462050\/original\/file-20220509-12-fxhj9p.png?ixlib=rb-1.1.0&amp;q=15&amp;auto=format&amp;w=600&amp;h=333&amp;fit=crop&amp;dpr=3 1800w, https:\/\/images.theconversation.com\/files\/462050\/original\/file-20220509-12-fxhj9p.png?ixlib=rb-1.1.0&amp;q=45&amp;auto=format&amp;w=754&amp;h=419&amp;fit=crop&amp;dpr=1 754w, https:\/\/images.theconversation.com\/files\/462050\/original\/file-20220509-12-fxhj9p.png?ixlib=rb-1.1.0&amp;q=30&amp;auto=format&amp;w=754&amp;h=419&amp;fit=crop&amp;dpr=2 1508w, https:\/\/images.theconversation.com\/files\/462050\/original\/file-20220509-12-fxhj9p.png?ixlib=rb-1.1.0&amp;q=15&amp;auto=format&amp;w=754&amp;h=419&amp;fit=crop&amp;dpr=3 2262w\"\/><\/noscript><\/a><figcaption><span class=\"caption\">AlphaFold2 can take the amino acid sequence of fluorescent proteins (letters at the top) and predict their 3D barrel shapes (middle). This isn\u2019t surprising. What is totally unexpected is that it can also predict which fluorescent proteins are \u2018broken\u2019 and can\u2019t fluoresce.<\/span><br \/><span class=\"attribution\"><span class=\"source\">Marc Zimmer<\/span>, <a rel=\"nofollow noopener\" target=\"_blank\" class=\"license\" href=\"https:\/\/creativecommons.org\/licenses\/by-nd\/4.0\/\">CC BY-ND<\/a><\/span><\/figcaption><\/figure>\n<p>The result stunned us: AlphaFold2 had learned some chemistry. It had figured out which amino acids in fluorescent proteins do the chemistry that makes them glow. We suspect that the protein databank training set and <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/samfordubioinformatics.wordpress.com\/bioinformatics-techniques\/multiple-sequence-alignment\/\">multiple sequence alignments<\/a> enable AlphaFold2 to \u201cthink\u201d like chemists and look for the amino acids required to react with one another to make the protein fluorescent.<\/p>\n<p>A folding program learning some chemistry from its training set also has wider implications. By asking the right questions, what else can be gained from other deep learning algorithms? Could facial recognition algorithms find hidden markers for diseases? Could algorithms designed to predict spending patterns among consumers also find a propensity for minor theft or deception? And most important, is this capability \u2013 and <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/www.technologyreview.com\/2019\/09\/17\/75427\/open-ai-algorithms-learned-tool-use-and-cooperation-after-hide-and-seek-games\/\">similar leaps in ability<\/a> in other AI systems \u2013 desirable?<!-- Below is The Conversation's page counter tag. Please DO NOT REMOVE. --><img loading=\"lazy\" style=\"border: none !important; box-shadow: none !important; margin: 0 !important; max-height: 1px !important; max-width: 1px !important; min-height: 1px !important; min-width: 1px !important; opacity: 0 !important; outline: none !important; padding: 0 !important;\" alt=\"The Conversation\" width=\"1\" height=\"1\" class=\"js-lazy\" https:=\"\"\/><!-- End of code. If you don't see any code above, please get new code from the Advanced tab after you click the republish button. The page counter does not collect any personal data. More info: https:\/\/theconversation.com\/republishing-guidelines --><\/p>\n<p><noscript><img loading=\"lazy\" style=\"border: none !important; box-shadow: none !important; margin: 0 !important; max-height: 1px !important; max-width: 1px !important; min-height: 1px !important; min-width: 1px !important; opacity: 0 !important; outline: none !important; padding: 0 !important;\" https:=\"\" alt=\"The Conversation\" width=\"1\" height=\"1\" class=\"\" srcset=\"\"\/><\/noscript><br \/>\n<em>This article by <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/theconversation.com\/profiles\/marc-zimmer-160444\">Marc Zimmer<\/a>, Professor of Chemistry, <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/theconversation.com\/institutions\/connecticut-college-1921\">Connecticut College<\/a>, is republished from <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/theconversation.com\">The Conversation<\/a> under a Creative Commons license. Read the <a rel=\"nofollow noopener\" target=\"_blank\" href=\"https:\/\/theconversation.com\/a-celebrated-ai-has-learned-a-new-trick-how-to-do-chemistry-182031\">original article<\/a>.<\/em>\n                        <\/div>\n<blockquote><p><strong><span style=\"color: #ff6600;\">If you liked the article, do not forget to share it with your friends. Follow us on\u00a0<span style=\"color: #ff0000;\"><a style=\"color: #ff0000;\" href=\"https:\/\/news.google.com\/publications\/CAAqBwgKMLG0nwswvr63Aw\" target=\"_blank\" rel=\"nofollow noopener noreferrer\">Google News<\/a><\/span>\u00a0too, click on the star and choose us from your favorites.<\/span><\/strong><\/p><\/blockquote>\n<blockquote>\n<p style=\"text-align: center;\">For forums sites go to <span style=\"color: #ff9900;\"><a style=\"color: #ff9900;\" href=\"https:\/\/forum.buradabiliyorum.com\/\" target=\"_blank\" rel=\"noopener\">Forum.BuradaBiliyorum.Com<\/a><\/span><\/strong>\n<\/p><\/blockquote>\n<blockquote>\n<p style=\"text-align: center;\"><strong>If you want to read more like this article, you can visit our <span style=\"color: #ff9900;\"><a style=\"color: #ff9900;\" href=\"https:\/\/en.buradabiliyorum.com\/technology\/\" target=\"_blank\" rel=\"noopener\">Technology category.<\/a><\/span><\/strong><\/p>\n<\/blockquote>\n<p><span style=\"color: black;\"><a style=\"color: #ff9900;\" href=\"https:\/\/thenextweb.com\/news\/a-celebrated-ai-has-learned-a-new-trick-how-to-do-chemistry\" target=\"_blank\" rel=\"noopener\">Source<\/a><\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>&#8220;A celebrated AI has learned a new trick: How to do\u00a0chemistry&#8221; Artificial intelligence has changed the way science is done by allowing researchers to analyze the massive amounts of data modern scientific instruments generate. It can find a needle in a million haystacks of information and, using deep learning, it can learn from the data&#8230;<\/p>\n","protected":false},"author":1,"featured_media":464920,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"fifu_image_url":"https:\/\/img-cdn.tnwcdn.com\/image\/neural?filter_last=1&fit=1280,640&url=https:\/\/cdn0.tnwcdn.com\/wp-content\/blogs.dir\/1\/files\/2022\/06\/shutterstock_1733742608-Protein-folding-hed.jpg&signature=f90a8fd366d297eded59735236f227ae","fifu_image_alt":"","footnotes":""},"categories":[18],"tags":[],"class_list":["post-464919","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-technology"],"_links":{"self":[{"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/posts\/464919","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/comments?post=464919"}],"version-history":[{"count":0,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/posts\/464919\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/media\/464920"}],"wp:attachment":[{"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/media?parent=464919"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/categories?post=464919"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/buradabiliyorum.com\/en\/wp-json\/wp\/v2\/tags?post=464919"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}