AlphaFold protein structures now on SGD protein pages

<!DOCTYPE html> <head> <meta http-equiv="Content-Type" content="text/html;charset=UTF-8"> <meta name="description" content="The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae."> <link rel="shortcut icon" type="image/x-icon" href="/img-domain/favicon.ico" /> <style type="text/css"> .locale { text-align: center; } .locale-name { font-weight: bold; } </style> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>AlphaFold protein structures now on SGD protein pages | SGD</title> <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.5.0/css/font-awesome.min.css" rel="stylesheet" type="text/css"> <link href="/static/css/normalize.css" rel="stylesheet"> <link href="/static/css/style.css" rel="stylesheet"> <script src="/static/js/build/modernizr.min.js"></script> </head> <body data-spy="scroll" data-target=".sgd-navbar">  <div id="j-application-target"> <header id="layout-page-header">  <div class="hide-for-small"> <div class="top-header"> <div> <span class="sgd-announcment"></span> </div> <div class="site-links"> <a target="_blank" href="https://sites.google.com/view/yeastgenome-help/about" class="hide-external-link-icon">About</a><a href="/blog">Blog</a><a href="http://sgd-archive.yeastgenome.org">Download</a><a href="https://www.yeastgenome.org/search?q=&is_quick=true">Explore</a><a class="hide-external-link-icon" target="_blank" href="https://sites.google.com/view/yeastgenome-help/sgd-general-help">Help</a><a href="https://www.alliancegenome.org/bluegenes/alliancemine">Get Data</a> <div class="social-media-links no-svg"> <a href="mailto:sgd-helpdesk@lists.stanford.edu" id="email-header" class="webicon mail small">Email Us</a> <a href="https://genomic.social/@yeastgenome" target="_blank" class="webicon mastodon small" id="mastodon">Mastodon</a> <a href="https://bsky.app/profile/yeastgenome.bsky.social" target="_blank" class="webicon bluesky small" id="bluesky">BlueSky</a> <a href="https://www.facebook.com/yeastgenome" target="_blank" class="webicon facebook small" id="facebook">Facebook</a> <a href="https://www.linkedin.com/company/saccharomyces-genome-database" target="_blank" class="webicon linkedin small" id="linkedin">LinkedIn</a> <a href="https://www.youtube.com/SaccharomycesGenomeDatabase" target="_blank" id="youtube" class="webicon youtube small">YouTube</a> </div> </div> </div> </div> <section> <div class="menu-bar-container"> <a href="/" class="show-for-large-up"> <div class="logo"><span class="logo-label">Saccharomyces Genome Database</span> </div> </a> <div class="sgd-menu-divider left show-for-large-up"></div> <div class="top-menu-container"> <nav class="top-bar" data-topbar="true" role="navigation"> <ul class="title-area"> <li class="name"><span class="hide-for-large-up"><a href="/" class="show-for-medium"><div class="logo small-logo"><span class="logo-label">Saccharomyces Genome Database</span> </div> </a> <a href="/" class="show-for-small"> <div class="logo small-logo"><span class="logo-label">Saccharomyces Genome Database</span> </div> </a> </span> </li> <li class="toggle-topbar menu-icon"><a href="#"><span>Menu</span></a> </li> </ul> <section class="top-bar-section"> <ul class="left"> <li class="has-dropdown"><a href="#">Analyze</a> <ul class="dropdown"> <li><a class="disabled-header-a" href="https://www.alliancegenome.org/bluegenes/alliancemine/upload/input">Gene Lists</a> </li> <li><a class="disabled-header-a" href="/blast-sgd">BLAST</a> </li> <li><a class="disabled-header-a" href="/blast-fungal">Fungal BLAST</a> </li> <li><a class="disabled-header-a" href="/goTermFinder">GO Term Finder</a> </li> <li><a class="disabled-header-a" href="/goSlimMapper">GO Slim Mapper</a> </li> <li><a class="disabled-header-a" href="/nph-patmatch">Pattern Matching</a> </li> <li><a class="disabled-header-a" href="/primer3">Design Primers</a> </li> <li><a class="disabled-header-a" href="/restrictionMapper">Restriction Site Mapper</a> </li> </ul> </li> <li class="has-dropdown"><a href="#">Sequence</a> <ul class="dropdown"> <li><a class="disabled-header-a" href="http://sgd-archive.yeastgenome.org/sequence/">Download</a> </li> <li><a class="disabled-header-a" href="https://jbrowse.yeastgenome.org">Genome Browser</a> </li> <li><a class="disabled-header-a" href="/blast-sgd">BLAST</a> </li> <li><a class="disabled-header-a" href="/blast-fungal">Fungal BLAST</a> </li> <li><a class="disabled-header-a" href="/seqTools">Gene/Sequence Resources</a> </li> <li class="has-dropdown"><a href="#">Reference Genome</a> <ul class="dropdown"> <li><a class="disabled-header-a" href="http://sgd-archive.yeastgenome.org/sequence/S288C_reference/genome_releases/">Download Genome</a> </li> <li><a class="disabled-header-a" href="/genomesnapshot">Genome Snapshot</a> </li> <li><a class="disabled-header-a" href="https://wiki.yeastgenome.org/index.php/Summary_of_Chromosome_Sequence_and_Annotation_Updates">Chromosome History</a> </li> <li><a class="disabled-header-a" href="https://wiki.yeastgenome.org/index.php/Systematic_Sequencing_Table">Systematic Sequencing Table</a> </li> <li><a class="disabled-header-a" href="https://wiki.yeastgenome.org/index.php/Original_Sequence_Papers">Original Sequence Papers</a> </li> </ul> </li> <li class="has-dropdown"><a href="#">Strains and Species</a> <ul class="dropdown"> <li><a class="disabled-header-a" href="/variant-viewer#/?_k=3yu0l3">Variant Viewer</a> <li><a class="disabled-header-a" href="/strainAlignment">Align Strain Sequences</a> </li> </ul> </li> <li class="has-dropdown"><a href="#">Resources</a> <ul class="dropdown"> <li><a class="disabled-header-a" href="http://www.uniprot.org/">UniProtKB</a> </li> <li><a class="disabled-header-a" href="http://www.ebi.ac.uk/interpro/">InterPro (EBI)</a> </li> <li><a class="disabled-header-a" href="http://www.ncbi.nlm.nih.gov/homologene">HomoloGene (NCBI)</a> </li> <li><a class="disabled-header-a" href="http://ygob.ucd.ie/">YGOB (Trinity College)</a> </li> <li><a class="disabled-header-a" href="https://alphafold.ebi.ac.uk/">AlphaFold</a> </li> </ul> </li> </ul> </li> <li class="has-dropdown"><a href="">Function</a> <ul class="dropdown"> <li class="has-dropdown"><a href="#">Gene Ontology</a> <ul class="dropdown"> <li><a class="disabled-header-a" href="/goTermFinder">GO Term Finder</a> </li> <li><a class="disabled-header-a" href="/goSlimMapper">GO Slim Mapper</a> </li> <li><a class="disabled-header-a" href="http://sgd-archive.yeastgenome.org/curation/literature/go_slim_mapping.tab">GO Slim Mapping File</a> </li> </ul> </li> <li><a class="disabled-header-a" href="https://spell.yeastgenome.org/">Expression</a> </li> <li><a class="disabled-header-a" href="https://pathway.yeastgenome.org">Biochemical Pathways</a> </li> <li class="has-dropdown"><a href="#">Phenotypes</a> <ul class="dropdown"> <li><a class="disabled-header-a" href="/ontology/phenotype/ypo">Browse All Phenotypes</a> </li> </ul> </li> <li><a class="disabled-header-a" href="/interaction-search">Interactions</a> </li> <li><a class="disabled-header-a" href="https://yeastgfp.yeastgenome.org/">YeastGFP</a> </li> <li class="has-dropdown"><a href="#">Resources</a> <ul class="dropdown"> <li><a class="disabled-header-a" href="http://www.geneontology.org/">GO Consortium</a> </li> <li><a class="disabled-header-a" href="http://thebiogrid.org/">BioGRID (U. Toronto)</a> </li> </ul> </li> </ul> </li> <li class="has-dropdown"><a href="">Literature</a> <ul class="dropdown"> <li><a class="disabled-header-a" href="https://www.alliancegenome.org/textpresso/sgd/tpc/search">Full-text Search</a> </li> <li><a class="disabled-header-a" href="/reference/recent">New Yeast Papers</a> </li> <li><a className="disabled-header-a" href="http://www.genetics.org/content/yeastbook">YeastBook</a></li> </li> <li class="has-dropdown"><a href="#">Resources</a> <ul class="dropdown"> <li><a class="disabled-header-a" href="http://www.ncbi.nlm.nih.gov/pubmed/">PubMed (NCBI)</a> </li> <li><a class="disabled-header-a" href="http://www.ncbi.nlm.nih.gov/pmc/">PubMed Central (NCBI)</a> </li> <li><a class="disabled-header-a" href="http://scholar.google.com/">Google Scholar</a> </li> </ul> </li> </ul> </li> <li class="has-dropdown"><a href="#">Community</a> <ul class="dropdown"> <li><a class="disabled-header-a" href="https://community.alliancegenome.org/categories">Community Forum</a> </li> <li class="has-dropdown"><a href="#">Colleague Information</a> <ul class="dropdown"> <li><a class="disabled-header-a" href="/search?q=&category=colleague">Find a Colleague</a> </li> <li><a href="/colleague_update">Add or Update Info</a> </li> <li><a class="disabled-header-a" href="/search?q=&category=colleague">Find a Yeast Lab</a> </li> </ul> </li> <li><a class="disabled-header-a" href="https://wiki.yeastgenome.org/index.php/Career_Resources">Career Resources</a> </li> <li><a class="disabled-header-a" href="https://wiki.yeastgenome.org/index.php/Educational_Resources">Education</a> </li> <li><a class="disabled-header-a" href="https://community.alliancegenome.org/c/model-organism-yeast/conferences/241">Meetings</a> </li> <li class="has-dropdown"><a href="#">Nomenclature</a> <ul class="dropdown"> <li><a class="disabled-header-a" href="/reserved_name/new">Submit a Gene Registration</a> </li> <li><a class="disabled-header-a" target="_blank" href="https://sites.google.com/view/yeastgenome-help/community-help/gene-registry">Gene Registry</a> </li> <li><a class="disabled-header-a" target="_blank" href="https://sites.google.com/view/yeastgenome-help/community-help/nomenclature-conventions">Nomenclature Conventions</a> </li> </ul> </li> <li class="has-dropdown"><a href="#">Methods and Reagents</a> <ul class="dropdown"> <li><a class="disabled-header-a" href="https://wiki.yeastgenome.org/index.php/Strains">Strains and Constructs</a> </li> <li><a class="disabled-header-a" href="https://wiki.yeastgenome.org/index.php/Reagents">Reagents</a> </li> <li><a class="disabled-header-a" href="https://wiki.yeastgenome.org/index.php/Methods">Protocols and Methods</a> </li> </ul> </li> <li class="has-dropdown"><a href="#">Historical Data</a> <ul class="dropdown"> <li><a class="disabled-header-a" href="https://wiki.yeastgenome.org/index.php/Combined_Physical_and_Genetic_Maps_of_S._cerevisiae">Physical & Genetic Maps</a> </li> <li><a class="disabled-header-a" href="https://wiki.yeastgenome.org/index.php/Yeast_Mortimer_Maps_-_Edition_12">Genetic Maps</a> </li> <li><a class="disabled-header-a" href="https://wiki.yeastgenome.org/index.php/Genetic_Loci">Genetic Loci</a> </li> <li><a class="disabled-header-a" href="https://wiki.yeastgenome.org/index.php/ORFmap_Images">ORFMap Chromosomes</a> </li> <li><a class="disabled-header-a" href="https://wiki.yeastgenome.org/index.php/Historical_Systematic_Sequence_Information">Sequence</a> </li> </ul> </li> <li><a class="disabled-header-a" href="/submitData">Submit Data</a></li> <li><a class="disabled-header-a" href="https://wiki.yeastgenome.org/index.php/External_Links">Resources</a> </li> <li><a class="disabled-header-a" href="/api/doc" target="_blank">API</a></li> </ul> </li> <li class="has-dropdown" id="info-menu"><a href="#">Info & Downloads</a> <ul class="dropdown"> <li><a class="disabled-header-a" href="https://sites.google.com/view/yeastgenome-help/about">About</a> </li> <li><a class="disabled-header-a" href="/blog">Blog</a> </li> <li><a class="disabled-header-a" href="/downloads">Downloads</a> </li> <li><a class="disabled-header-a" href="/site-map">Site Map</a> </li> <li><a class="disabled-header-a"target="_blank" href="https://sites.google.com/view/yeastgenome-help/sgd-general-help">Help</a> </li> </ul> </li> </ul> </section> </nav> </div> <div class="sgd-menu-divider right show-for-large-up"></div> <div class="menu-search-container" id="j-search-container"> <div class="sgd-search-container"> <form action='/search' autocomplete='off'> <div style="position:relative;" class="react-typeahead-container "> <div style="position:relative;" class="react-typeahead-input-container"> <input disabled="" role="presentation" aria-hidden="true" class="react-typeahead-input react-typeahead-hint" style="color:silver;-webkit-text-fill-color:silver;position:absolute;" /> <input autocomplete="false" role="combobox" placeholder="search: actin, kinase, glucose" style="position:relative;background:transparent;" spellcheck="false" value="" aria-owns="react-typeahead-options-1" aria-autocomplete="both" autocorrect="false" aria-expanded="false" aria-activedescendant="react-typeahead-activedescendant-1" class="react-typeahead-input react-typeahead-usertext" name="q" autocomplete="off" /> </div><span role="status" aria-live="polite" style="left:-9999px;position:absolute;"></span><span role="status" aria-live="polite" style="left:-9999px;position:absolute;"></span> </div> <input type="submit" style="display:none;"> </form> <span class="search-icon"><i class="fa fa-search"></i></span> </div> </div> </div> </section> </header> <div class="container" id="layout-document"> <div class="row"> <div class="columns medium-2 hide-for-small-only"> <div class="simple-list"> <p>Categories</p> <ul> <li><a href="/blog/category/announcements">Announcements</a></li> <li><a href="/blog/category/conferences">Conferences</a></li> <li><a href="/blog/category/data-updates">Data updates</a></li> <li><a href="/blog/category/homologs">Homologs</a></li> <li><a href="/blog/category/new-data">New Data</a></li> <li><a href="/blog/category/news-and-views">News and Views</a></li> <li><a href="/blog/category/newsletter">Newsletter</a></li> <li><a href="/blog/category/research-spotlight">Research Spotlight</a></li> <li><a href="/blog/category/sequence">Sequence</a></li> <li><a href="/blog/category/tutorial">Tutorial</a></li> <li><a href="/blog/category/uncategorized">Uncategorized</a></li> <li><a href="/blog/category/website-changes">Website changes</a></li> <li><a href="/blog/category/yeast-and-human-disease">Yeast and Human Disease</a></li> </ul> <p>Archives</p> <ul> <li><a href="/blog/archive/2024">2024</a></li> <li><a href="/blog/archive/2023">2023</a></li> <li><a href="/blog/archive/2022">2022</a></li> <li><a href="/blog/archive/2021">2021</a></li> <li><a href="/blog/archive/2020">2020</a></li> <li><a href="/blog/archive/2019">2019</a></li> <li><a href="/blog/archive/2018">2018</a></li> </ul> </div> </div> <div class="columns small-12 medium-10"> <h1>New & Noteworthy</h1> <h2>AlphaFold protein structures now on SGD protein pages</h2> <div class="addthis_toolbox addthis_default_style"> <a class="addthis_button_facebook_like" fb:like:layout="button_count"></a><a class="addthis_button_tweet"></a> </div> <p>November 18, 2024</p> <p>We are thrilled to announce that we have now integrated <a href="https://alphafold.ebi.ac.uk">AlphaFold</a> protein structures into our <a href="https://www.yeastgenome.org/locus/set1/protein">protein</a> pages! This cutting-edge addition provides detailed, high-accuracy 3D models of protein structures, offering invaluable insights into protein function and interactions. Researchers can now explore these comprehensive structural predictions directly within SGD, facilitating advanced studies in molecular biology and bioinformatics. Dive into the new AlphaFold protein structures and elevate your research with this powerful tool!</p> <figure class="wp-block-image size-large"><img data-attachment-id="15051" data-permalink="https://yeastgenomeblog.wordpress.com/2024/11/18/alphafold-protein-structures-now-on-sgd-protein-pages/screenshot-2024-11-18-at-12-50-48-pm/" data-orig-file="https://yeastgenomeblog.wordpress.com/wp-content/uploads/2024/11/screenshot-2024-11-18-at-12.50.48e280afpm.png" data-orig-size="780,735" data-comments-opened="1" data-image-meta="{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}" data-image-title="Screenshot 2024-11-18 at 12.50.48鈥疨M" data-image-description="" data-image-caption="" data-medium-file="https://yeastgenomeblog.wordpress.com/wp-content/uploads/2024/11/screenshot-2024-11-18-at-12.50.48e280afpm.png?w=300" data-large-file="https://yeastgenomeblog.wordpress.com/wp-content/uploads/2024/11/screenshot-2024-11-18-at-12.50.48e280afpm.png?w=780" loading="lazy" width="780" height="735" src="https://yeastgenomeblog.wordpress.com/wp-content/uploads/2024/11/screenshot-2024-11-18-at-12.50.48e280afpm.png?w=780" alt="" class="wp-image-15051" /></figure> <p>AlphaFold, developed by聽<a href="https://deepmind.google/technologies/alphafold/">DeepMind</a>, is an AI program that accurately predicts protein structures from amino acid sequences, enabling visualization of protein conformations. The predicted structures can be accessed through the Protein Data Bank (<a href="https://www.rcsb.org/">PDB</a>) and聽<a href="https://alphafold.ebi.ac.uk/">AlphaFold Protein Structure Database</a>.</p> <p>Thanks to Kim Rutherford and Val Wood of <a href="https://www.pombase.org">Pombase</a> for tips about adding AlphaFold structures to SGD.</p> <p> Categories: <span><a href="/blog/category/announcements">Announcements</a></span> </p> </div> </div> <div id="layout-document-footer-pusher"></div> </div> <footer id="layout-document-footer" class="page-footer"> <div class="row"> <div class="small-5 large-5 columns"> <ul id="footer-links"> <li class="sgd-link"><a href="http://www.yeastgenome.org">SGD</a></li> <li><a class="hide-external-link-icon" target="_blank" href="https://sites.google.com/view/yeastgenome-help/about"><span>About</span></a></li> <li><a href="http://www.yeastgenome.org/blog"><span>Blog</span></a></li> <li><a class="hide-external-link-icon" target="_blank" href="https://sites.google.com/view/yeastgenome-help/sgd-general-help"><span>Help</span></a></li> <li><a class="hide-external-link-icon" target="_blank" href="http://www.stanford.edu/site/privacy"><span>Privacy Policy</span></a></li> <li><a rel="license" class="hide-external-link-icon" target="_blank" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a></li> <li id="social-footer"> <ul class="social-links"> <li><a href="/cgi-bin/suggestion" target="_blank" id="email-footer" class="webicon mail small">Email Us</a></li> <li><a href="http://twitter.com/#!/yeastgenome" target="_blank" id="twitter-footer" class="webicon twitter small">Twitter</a></li> <li><a href="https://www.facebook.com/pages/Saccharomyces-Genome-Database-SGD/139140876128200" target="_blank" class="webicon facebook small" id="facebook-footer">Facebook</a></li> <li><a href="https://www.linkedin.com/company/saccharomyces-genome-database" target="_blank" class="webicon linkedin small" id="linkedin-footer">LinkedIn</a></li> <li><a href="https://www.youtube.com/SaccharomycesGenomeDatabase" target="_blank" id="youtube-footer" class="webicon youtube small">YouTube</a></li> </ul> </li> </ul> <div id="copyright">© Stanford University, Stanford, CA 94305.</div> </div> <div class="small-7 large-7 columns"> <ul class="logo-list"> <li> <a href="https://www.alliancegenome.org"> <img height="55" width="110" src="/static/img/agr_logo.png" id="agr-logo"> </a> </li> <li><a href="https://globalbiodata.org/scientific-activities/global-core-biodata-resources/"> <img height="45" width="100" src="/static/img/GCBR-Logo-White.svg" id="gcbr-logo"> </a></li> <li><a href="https://med.stanford.edu/genetics.html"> <img height="45" width="80" src="/static/img/genetics-logo@2x.png" id="genetics-logo"> </a></li> <li><a href="https://med.stanford.edu/"> <img height="45" width="39" src="/static/img/som-logo@2x.png" id="som-logo"> </a></li> <li><a href="https://www.stanford.edu/"><img height="45" width="80" src="/static/img/footer-stanford-logo@2x.png" id="stanford-logo"></a></li> </ul> </div> </div> </footer> </div>    <script src="//ajax.googleapis.com/ajax/libs/jquery/1.11.1/jquery.min.js"></script> <script>window.jQuery || document.write('<script src="/static/js/build/jquery.min.js"><\/script>')</script> <script>window.ASSET_ROOT = "/static";</script> <script src="/static/js/application.js"></script>  <script> (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); ga('create', 'UA-440742-1', 'yeastgenome.org'); ga('send', 'pageview'); </script>   <script async src="https://www.googletagmanager.com/gtag/js?id=G-BX4ZG9DC05"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'G-BX4ZG9DC05'); </script> <script type="text/javascript" src="//s7.addthis.com/js/300/addthis_widget.js#pubid=ra-589e356ccacdcbaf"></script> </body> </html>

CINXE.COM

AlphaFold protein structures now on SGD protein pages | SGD