{"id":46680,"date":"2022-02-01T15:00:00","date_gmt":"2022-02-01T14:00:00","guid":{"rendered":"https:\/\/www.embl.org\/news\/?p=46680"},"modified":"2024-03-22T15:27:34","modified_gmt":"2024-03-22T14:27:34","slug":"decoding-the-secrets-of-snake-venom","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/decoding-the-secrets-of-snake-venom\/","title":{"rendered":"Decoding the secrets of snake venom"},"content":{"rendered":"\n<p>The lancehead snake <em>Bothrops atrox<\/em> is responsible for the majority of snakebites in the Amazon region of South America. Snakebites, which can cause serious damage to health or even death, happen particularly frequently in poor rural areas and count among neglected tropical diseases. Studying the composition of venoms can help scientists develop new antivenoms to treat snakebites. For this, it is critical to understand the structure of proteins that are active components of snake venom.<\/p>\n\n\n\n<p>Scientists at EMBL Hamburg have now created a tool that will make structural biology studies on snake venoms and other naturally extracted samples significantly easier. Such samples often contain unknown proteins that are hard to identify without additional experiments. Grzegorz Chojnowski from the Wilmanns Group developed a neural-network-based program called <em><a href=\"https:\/\/gitlab.com\/gchojnowski\/findmysequence\">findMySequence<\/a><\/em>, which identifies the amino-acid sequences of proteins based only on electron cryo-microscopy and X-ray crystallography data. An unknown protein found in the <em>B. atrox<\/em>\u2019s venom was the perfect sample for testing the software.&nbsp;<\/p>\n\n\n\n<p>\u201cThe program is really useful when you study samples from natural sources, such as snake venom, because you can never be sure what you will find there,\u201d said Chojnowski. \u201cIt\u2019s also great for cryo-EM experiments in which you study a molecule in its cellular environment, surrounded by a molecular crowd.\u201d<\/p>\n\n\n\n<p><em>findMySequence<\/em> can complement the ground-breaking <a href=\"https:\/\/www.embl.org\/news\/science\/thornton-alphafold\/\">AI-based AlphaFold2<\/a> algorithm, which makes protein structure predictions based on its amino-acid sequence. The program has already contributed, among others, to determining the structure of a <a href=\"https:\/\/www.embl.org\/news\/science\/structural-biology-reveals-new-opportunities-to-combat-tuberculosis\/\">molecular complex involved in tuberculosis<\/a>, and to <a href=\"https:\/\/www.cell.com\/structure\/fulltext\/S0969-2126(22)00001-6\">studying protein communities in cell extracts<\/a>.<\/p>\n\n\n\n<p>This work is an example of how the complexity of biology in nature can be studied at the molecular level &#8211; an important concept explored in the new <a href=\"https:\/\/www.embl.org\/about\/programme\/\">EMBL Programme \u2018Molecules to Ecosystems\u2019<\/a>, launched in 2022.<\/p>\n\n\n\n<p>The study was performed in collaboration with scientists from EMBL Heidelberg, University of S\u00e3o Paulo in Brazil, Universidad Nacional Mayor de San Marcos in Peru, and University of Liverpool and Rutherford Appleton Laboratory in the UK. Crystals of the venom protein were analysed at the Brazilian National Laboratory of Synchrotron Light, part of the National Center for Energy and Materials.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>EMBL Hamburg\u2019s Grzegorz Chojnowski from the Wilmanns Group developed software called findMySequence, which identifies proteins\u2019 amino-acid sequences based on electron cryo-microscopy and X-ray crystallography data. It\u2019s useful for identifying unknown proteins in samples from natural sources.<\/p>\n","protected":false},"author":96,"featured_media":46714,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[2,17591],"tags":[189,53,12760,5752,3618,35,306],"embl_taxonomy":[9596,19403],"class_list":["post-46680","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science","category-science-technology","tag-computational-biology","tag-hamburg","tag-latin-america","tag-protein-structure","tag-software","tag-structural-biology","tag-wilmanns","embl_taxonomy-embl-hamburg","embl_taxonomy-wilmanns-group"],"acf":{"featured":true,"show_featured_image":false,"field_target_display":"embl","article_intro":"<p>A neural-network-based program developed at EMBL Hamburg identified an unknown protein in snake venom<\/p>\n","related_links":[{"link_description":"Download findMySequence ","link_url":"https:\/\/gitlab.com\/gchojnowski\/findmysequence"},{"link_description":"Wilmanns Group ","link_url":"https:\/\/www.embl.org\/groups\/wilmanns\/"},{"link_description":"EMBL Programme ","link_url":"https:\/\/www.embl.org\/about\/programme\/"}],"source_article":[{"publication_title":"findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM","publication_link":{"title":"","url":"https:\/\/journals.iucr.org\/m\/issues\/2022\/01\/00\/pw5018\/","target":"_blank"},"publication_authors":"Chojnowski G., et al.","publication_source":"IUCrJ","publication_date":"9 December 2021","publication_doi":"10.1107\/S2052252521011088"}],"in_this_article":false,"press_contact":"None","vf_locked":false},"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:\"613c4de5-1775-447f-af71-4b07085318e9\";}","parents":[],"name":["EMBL Hamburg"],"slug":"embl-hamburg","description":"Where &gt; All EMBL sites &gt; EMBL Hamburg"},{"uuid":"a:3:{i:0;s:36:\"302cfdf7-365b-462a-be65-82c7b783ebf7\";i:1;s:36:\"2dc39890-6c01-47bf-ac78-d42abdb10079\";i:2;s:36:\"b7081976-e7c1-4678-ab00-3e02d20e9e87\";}","parents":[],"name":["Wilmanns Group"],"slug":"wilmanns-group","description":"What &gt; Structural Biology (EMBL Hamburg) &gt; Wilmanns Group"}],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Decoding the secrets of snake venom | EMBL<\/title>\n<meta name=\"description\" content=\"Software findMySequence developed at EMBL Hamburg identifies proteins\u2019 amino-acid sequences based on their 3D molecular structure.\" \/>\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\/decoding-the-secrets-of-snake-venom\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Decoding the secrets of snake venom | EMBL\" \/>\n<meta property=\"og:description\" content=\"Software findMySequence developed at EMBL Hamburg identifies proteins\u2019 amino-acid sequences based on their 3D molecular structure.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.embl.org\/news\/science\/decoding-the-secrets-of-snake-venom\/\" \/>\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=\"2022-02-01T14:00:00+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2024-03-22T14:27:34+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2022\/01\/AdobeStock_376253485-snake_Bothrops_atrox-1000x600-1.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=\"Dorota Badowska\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@d_badowska\" \/>\n<meta name=\"twitter:site\" content=\"@embl\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Dorota Badowska\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"2 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\/decoding-the-secrets-of-snake-venom\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/decoding-the-secrets-of-snake-venom\/\"},\"author\":{\"name\":\"Dorota Badowska\",\"@id\":\"https:\/\/www.embl.org\/news\/#\/schema\/person\/b8ae50efcd7533f0ab2ec368736b1d04\"},\"headline\":\"Decoding the secrets of snake venom\",\"datePublished\":\"2022-02-01T14:00:00+00:00\",\"dateModified\":\"2024-03-22T14:27:34+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/decoding-the-secrets-of-snake-venom\/\"},\"wordCount\":358,\"publisher\":{\"@id\":\"https:\/\/www.embl.org\/news\/#organization\"},\"image\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/decoding-the-secrets-of-snake-venom\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2022\/01\/AdobeStock_376253485-snake_Bothrops_atrox-1000x600-1.jpg\",\"keywords\":[\"computational biology\",\"hamburg\",\"latin america\",\"protein structure\",\"software\",\"structural biology\",\"wilmanns\"],\"articleSection\":[\"Science\",\"Science &amp; 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