{"id":1250,"date":"2024-12-24T06:16:42","date_gmt":"2024-12-24T06:16:42","guid":{"rendered":"https:\/\/amm-journal.org\/?p=1250"},"modified":"2024-12-24T06:16:42","modified_gmt":"2024-12-24T06:16:42","slug":"adversarial-sequence-mutations-in-alphafold2","status":"publish","type":"post","link":"https:\/\/amm-journal.org\/index.php\/2024\/12\/24\/adversarial-sequence-mutations-in-alphafold2\/","title":{"rendered":"AF2-mutation: adversarial sequence mutations against AlphaFold2 in protein tertiary structure prediction"},"content":{"rendered":"<p>Announcing a new publication for <a href=\"https:\/\/amm-journal.org\/\"><em>Acta Materia Medica<\/em> journal<\/a>. Proteins are essential macromolecules that perform functions according to their conformational dynamics. Studying the conformational changes induced by protein mutations is the standard approach used to understand the mechanisms underlying mutation-related physiological and pathological processes. To enhance efficiency and decrease the expense of biological experiments, this paper introduces a method to generate mutated proteins through adversarial attacks on the AlphaFold2 (AF2) model. The structure change of adversarial protein sequences predicted by AF2 were explored compared to the wild type protein\u2019s structure. CASP14 experiments indicated that altering only three residues via replacement, deletion, or insertion led to a 46.61 points difference in AF2\u2019s predictions, according to the Local Distance Difference Test (lDDT). The method was applied to the transmembrane lipid transporter SPNS2 to identify crucial residues and suggest potential alternative conformations, thereby streamlining the experimental phase in structure determination and mechanistic studies.<\/p>\n<p>Read more at <a href=\"https:\/\/www.scienceopen.com\/hosted-document?doi=10.15212\/AMM-2024-0047\">ScienceOpen<\/a>: <a href=\"https:\/\/www.scienceopen.com\/hosted-document?doi=10.15212\/AMM-2024-0047\">https:\/\/www.scienceopen.com\/hosted-document?doi=10.15212\/AMM-2024-0047<\/a><\/p>\n<p><em>Acta Materia Medica<\/em> welcomes the submission of research articles, review articles, databases, mini reviews, commentaries, editorials, short communications, case report articles and study protocols.<\/p>\n<p><strong>Submission Process<\/strong><\/p>\n<p>Submissions <em>to Acta Materia Medica<\/em> are made using ScholarOne, the online submission and peer review system. Registration and access are available at <a href=\"https:\/\/mc04.manuscriptcentral.com\/ammed\">https:\/\/mc04.manuscriptcentral.com\/ammed<\/a><\/p>\n<p>Queries about the journal can be sent to editorialoffice@amm-journal.org.<\/p>\n<p>Please visit <a href=\"https:\/\/amm-journal.org\/\">https:\/\/amm-journal.org\/<\/a> to learn more about the journal.<\/p>\n<p><strong>Editorial Board:<\/strong> <a href=\"https:\/\/amm-journal.org\/index.php\/editorial-board\/\">https:\/\/amm-journal.org\/index.php\/editorial-board\/<\/a><\/p>\n<p>There are no author submission or article processing fees.<\/p>\n<p>Follow <strong><em>Acta Materia Medica <\/em><\/strong>on Twitter <a href=\"https:\/\/twitter.com\/AMM_journal\">https:\/\/twitter.com\/AMM_journal<\/a>; <a href=\"https:\/\/www.facebook.com\/Zoonoses-Journal-100462755574114\">Facebook<\/a> (<a href=\"https:\/\/www.facebook.com\/AMMjournal\">https:\/\/www.facebook.com\/AMMjournal<\/a>)<\/p>\n<p><strong>eISSN <\/strong>2737-7946<\/p>\n<p>Zhongju Yuan, Tao Shen and Sheng Xu et al. AF2-mutation: adversarial sequence mutations against AlphaFold2 in protein tertiary structure prediction.\u00a0<em>Acta Materia Medica.\u00a0<\/em>2024. Vol. 3(4):462-476. DOI: 10.15212\/AMM-2024-0047<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Announcing a new publication for Acta Materia Medica journal. Proteins are essential macromolecules that perform functions according to their conformational dynamics. Studying the conformational changes induced by protein mutations is the standard approach used to understand the mechanisms underlying mutation-related physiological and pathological processes. To enhance efficiency and decrease the expense of biological experiments, this [&hellip;]<\/p>\n","protected":false},"author":5,"featured_media":1251,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[2],"tags":[361,363,360,362,334],"class_list":["post-1250","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-news-and-events","tag-adversarial-attack","tag-adversarial-sequence-mutations","tag-alphafold2","tag-mutation","tag-structural-biology"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>AF2-mutation: adversarial sequence mutations against AlphaFold2 in protein tertiary structure prediction<\/title>\n<meta name=\"description\" content=\"Discover how adversarial sequence mutations challenge AlphaFold2 in protein tertiary structure prediction, streamlining biological 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