{"id":62621,"date":"2023-09-13T17:03:40","date_gmt":"2023-09-13T15:03:40","guid":{"rendered":"https:\/\/www.embl.org\/news\/?p=62621"},"modified":"2024-03-22T11:44:04","modified_gmt":"2024-03-22T10:44:04","slug":"revealing-the-secrets-of-protein-evolution-using-the-alphafold-database","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/revealing-the-secrets-of-protein-evolution-using-the-alphafold-database\/","title":{"rendered":"Revealing the secrets of protein evolution using the AlphaFold database"},"content":{"rendered":"\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n      Summary    <\/h3>\n                <p class=\"vf-card__text\"><!-- wp:list -->\r\n<ul><!-- wp:list-item -->\r\n \t<li>Using the AlphaFold database and a new algorithm called Foldseek Cluster, researchers have analysed over 200 million predicted protein structures, identifying unique evolutionary patterns.<\/li>\r\n<!-- \/wp:list-item --> <!-- wp:list-item -->\r\n \t<li>The study uncovers new insights into the evolution of human immunity proteins by revealing structural similarities between human and bacterial proteins.<\/li>\r\n<!-- \/wp:list-item --> <!-- wp:list-item -->\r\n \t<li>As the AlphaFold database continues to expand, algorithms such as Foldseek Cluster emerge as critical tools for navigating and interpreting the wealth of information made available by AI predictions.<\/li>\r\n<!-- \/wp:list-item --><\/ul>\r\n<!-- \/wp:list --><\/p>\n      <\/div>\n<\/article>\n\n\n\n\n<p>By developing an efficient way to compare all predicted protein structures in the <a href=\"https:\/\/alphafold.ebi.ac.uk\/\">AlphaFold database<\/a>, researchers have revealed similarities between proteins across different species. This work aids our understanding of protein evolution and has uncovered new insights into the origin of human immunity proteins.&nbsp;<\/p>\n\n\n\n<p>The research was conducted by EMBL\u2019s European Bioinformatics Institute (EMBL-EBI), the Institute of Molecular Systems Biology ETH Zurich, and the School of Biological Sciences Seoul National University.<\/p>\n\n\n\n<p>The AlphaFold database is a transformative resource in the field of protein research, serving as a comprehensive repository of AI-predicted 3D structures for all known proteins. The database fills a critical gap in understanding protein function and evolution by offering high-quality structural predictions. Although AI predictions are not a substitute for experimentally determined structures, they do provide invaluable insights for the scientific community.<\/p>\n\n\n\n<p>For this study, <a href=\"https:\/\/www.nature.com\/articles\/s41586-023-06510-w\">published in the journal <em>Nature<\/em><\/a>, the researchers developed a new algorithm known as <a href=\"https:\/\/cluster.foldseek.com\/\">Foldseek Cluster<\/a> that can be used to analyse large sets of protein structures all at once. Foldseek Cluster was applied to the 200 million predicted protein structures in the AlphaFold database, identifying over 2 million unique structural clusters \u2013 groups of protein structures that are similar to each other in their three-dimensional shapes. One third of these clusters lack any previous annotations, meaning they had not before been described or categorised.<\/p>\n\n\n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n      AlphaFold Clusters database    <\/h3>\n                <p class=\"vf-card__text\">Explore the clustered AlphaFold protein structures analysed using Foldseek Cluster in the <a class=\"vf-card_link\" href=\"https:\/\/cluster.foldseek.com\/\">AlphaFold Clusters database<\/a>.<\/p>\n      <\/div>\n<\/article>\n\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Bridging the gap in protein science<\/strong><\/h2>\n\n\n\n<p>Proteins are critical to processes that take place in the cell. Understanding protein structure is pivotal for studying their function and evolution. Despite significant advancements in sequence-based predictions of protein structures, computational limitations have made it difficult to study these structures at scale. Foldseek Cluster now enables structural comparisons and clustering at an unprecedented scale, reducing the time for such tasks by several orders of magnitude.<\/p>\n\n\n\n<p>\u201cWe\u2019ve entered a new era in structural biology where computational methods unlock unprecedented access to explore the protein universe,\u201d said <a href=\"https:\/\/steineggerlab.com\/en\/\">Martin Steinegger, Assistant Professor at the School of Biological Sciences Seoul National University.<\/a> \u201cWe estimated that clustering all structures with established methods would have taken a decade when compared to the five days it took using our new method, Foldseek Cluster. Our algorithm can sift through millions of predicted protein structures in the AlphaFold database and cluster them based on their 3D shapes. This acceleration in computational power doesn\u2019t just make things faster; it makes things possible.\u201d<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Protein evolution and immunity<\/strong><\/h2>\n\n\n\n<p>The study also delves into the evolutionary implications of these clusters. While most clusters are ancient in origin, around 4% appear to be species-specific. This offers new insights into evolutionary phenomena such as <em>de novo<\/em> gene birth \u2013 when new genes arise from non-coding regions of the genome. The work also illustrates several examples of evolutionary relationships that could enrich our understanding of protein function across different species, including their role in human immunity.<\/p>\n\n\n\n<p>\u201cThis work isn&#8217;t just about making comparisons more efficiently, it&#8217;s about gaining new insights into the evolutionary history of proteins,\u201d said <a href=\"https:\/\/imsb.ethz.ch\/research\/beltrao.html\">Pedro Beltrao, Associate Professor at the Institute of Molecular Systems Biology, ETH Zurich<\/a>. \u201cOne of the most interesting findings from this study is our detection of structural similarities between human immune system proteins and those found in bacteria. This suggests that proteins involved in the immune system may have ancient evolutionary origins that we share with bacterial species. If true, this could reshape our understanding of immunity. Our research not only advances current knowledge but also lays out a roadmap for future investigations into the mysteries of protein function and evolution.&#8221;<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Improving the AlphaFold database functionality<\/strong><\/h2>\n\n\n\n<p>As the AlphaFold database and other life science databases continue to grow there is a significant need to help users sift through the vast amount of data while reducing the computational costs of analysing and managing these data. Approaches such as the Foldseek Cluster algorithm, that is scalable to billions of structures, will be invaluable in helping researchers navigate this wealth of information.<\/p>\n\n\n\n<p>&#8220;Foldseek Cluster is more than just a technological advancement; it&#8217;s an enhancement that elevates the entire AlphaFold database experience for researchers worldwide,\u201d said <a href=\"https:\/\/www.ebi.ac.uk\/people\/person\/sameer-velankar\/\">Sameer Velankar, Team Leader at EMBL-EBI<\/a>. \u201cWith the explosion of predicted protein structures we have in AFDB, managing and navigating these data efficiently has been a significant challenge,\u201d he continued. \u201cFoldseek Cluster has revolutionised this process. We are working on integrating FoldSeek clusters into AFDB to streamline the analysis of large sets of protein structures and make it easier for our user community to find exactly what they&#8217;re looking for.&#8221;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Researchers use the AlphaFold database and Foldseek Cluster algorithm to analyse millions of predicted protein structures and offer new insights into protein evolution.<\/p>\n","protected":false},"author":77,"featured_media":62639,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[11060,2,17591],"tags":[12758,4718,28,36,35,17281],"embl_taxonomy":[2906,19105],"class_list":["post-62621","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-research-highlights","category-science","category-science-technology","tag-alphafold","tag-artificial-intelligence","tag-bioinformatics","tag-embl-ebi","tag-structural-biology","tag-velankar","embl_taxonomy-embl-ebi","embl_taxonomy-sameer-velankar"],"acf":{"featured":true,"show_featured_image":false,"field_target_display":"both","field_article_language":{"value":"english","label":"English"},"article_intro":"<p>Researchers use the AlphaFold database and Foldseek Cluster algorithm to analyse millions of predicted protein structures and offer new insights into protein evolution<\/p>\n","related_links":[{"link_description":"AlphaFold Protein Structure Database","link_url":"https:\/\/alphafold.ebi.ac.uk\/"},{"link_description":"AlphaFold Clusters Database","link_url":"https:\/\/cluster.foldseek.com\/"}],"source_article":[{"publication_title":"Clustering-predicted structures at the scale of the known protein universe","publication_link":{"title":"","url":"https:\/\/www.nature.com\/articles\/s41586-023-06510-w","target":""},"publication_authors":"Barrio-Hernandez., I et al.","publication_source":"Nature","publication_date":"13 September 2023","publication_doi":"10.1038\/s41586-023-06510-w"}],"in_this_article":false,"press_contact":"None","article_translations":false,"languages":""},"embl_taxonomy_terms":[{"uuid":"a:3:{i:0;s:36:\"b14d3f13-5670-44fb-8970-e54dfd9c921a\";i:1;s:36:\"89e00fee-87f4-482e-a801-4c3548bb6a58\";i:2;s:36:\"a99d1a7c-ca83-4c00-ab61-d082d3e41ce3\";}","parents":[],"name":["EMBL-EBI"],"slug":"embl-ebi","description":"Where &gt; All EMBL sites &gt; EMBL-EBI"},{"uuid":"a:2:{i:0;s:36:\"4428d1fd-441a-4d6d-a1c5-5dcf5665f213\";i:1;s:36:\"ad573c35-01af-4a5a-a27c-bc4dbd27f694\";}","parents":[],"name":["Sameer Velankar"],"slug":"sameer-velankar","description":"Who &gt; Sameer Velankar"}],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Revealing the secrets of protein evolution using the AlphaFold database | EMBL<\/title>\n<meta name=\"description\" content=\"Researchers use the AlphaFold database and Foldseek Cluster algorithm to analyse millions of predicted protein structures and offer new insights into protein evolution\" \/>\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\/revealing-the-secrets-of-protein-evolution-using-the-alphafold-database\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Revealing the secrets of protein evolution using the AlphaFold database | EMBL\" \/>\n<meta property=\"og:description\" content=\"Researchers use the AlphaFold database and Foldseek Cluster algorithm to analyse millions of predicted protein structures and offer new insights into protein evolution\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.embl.org\/news\/science\/revealing-the-secrets-of-protein-evolution-using-the-alphafold-database\/\" \/>\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=\"2023-09-13T15:03:40+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2024-03-22T10:44:04+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/09\/2023-AlphaFold-Nature-1000x600-v1.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"1000\" \/>\n\t<meta property=\"og:image:height\" content=\"600\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"author\" content=\"Vicky Hatch\" \/>\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=\"Vicky Hatch\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. 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\":\"NewsArticle\",\"@id\":\"https:\/\/www.embl.org\/news\/science\/revealing-the-secrets-of-protein-evolution-using-the-alphafold-database\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/revealing-the-secrets-of-protein-evolution-using-the-alphafold-database\/\"},\"author\":{\"name\":\"Vicky Hatch\",\"@id\":\"https:\/\/www.embl.org\/news\/#\/schema\/person\/d8477ba2d7a6164b141a3872a25ee982\"},\"headline\":\"Revealing the secrets of protein evolution using the AlphaFold database\",\"datePublished\":\"2023-09-13T15:03:40+00:00\",\"dateModified\":\"2024-03-22T10:44:04+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/revealing-the-secrets-of-protein-evolution-using-the-alphafold-database\/\"},\"wordCount\":754,\"publisher\":{\"@id\":\"https:\/\/www.embl.org\/news\/#organization\"},\"image\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/revealing-the-secrets-of-protein-evolution-using-the-alphafold-database\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/09\/2023-AlphaFold-Nature-1000x600-v1.jpg\",\"keywords\":[\"alphafold\",\"artificial intelligence\",\"bioinformatics\",\"embl-ebi\",\"structural biology\",\"velankar\"],\"articleSection\":[\"Research highlights\",\"Science\",\"Science &amp; 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