{"id":20647,"date":"2025-01-10T11:17:24","date_gmt":"2025-01-10T10:17:24","guid":{"rendered":"https:\/\/sano.science\/?post_type=research&#038;p=20647"},"modified":"2025-01-10T13:44:35","modified_gmt":"2025-01-10T12:44:35","slug":"large-protein-databases-reveal-structural-complementarity-and-functional-locality","status":"publish","type":"research","link":"https:\/\/sano.science\/research\/large-protein-databases-reveal-structural-complementarity-and-functional-locality\/","title":{"rendered":"Large protein databases reveal structural complementarity and functional locality"},"content":{"rendered":"\n<h2 class=\"wp-block-heading eplus-wrapper\" id=\"h-pawel-szczerbiak-lukasz-m-szydlowski-witold-wydmanski-p-douglas-renfrew-julia-koehler-leman-tomasz-kosciolek\">Pawe\u0142 Szczerbiak, Lukasz M. Szydlowski, Witold Wydma\u0144ski, P. Douglas Renfrew, Julia Koehler Leman, Tomasz Kosciolek<\/h2>\n\n\n\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n\n\n\n<p class=\" eplus-wrapper\">Advances in protein structure prediction have resulted in a remarkable rise in high-quality 3D models, emphasizing the need for effective computational methods to handle and explore this structural data. Our study explores structural clusters derived from the AlphaFold Protein Structure Database (AFDB), a high-quality subset of ESMAtlas, and the Microbiome Immunity Project (MIP). We generate a unified low-dimensional representation of the protein structure space, revealing that while each database occupies distinct regions, they share significant overlap in functional profiles. Key biological functions cluster within specific regions, indicating a common functional landscape across diverse datasets. To support data exploration, we developed an open-access web server. These findings provide a foundation for further research into protein sequence-structure-function relationships, including taxonomic classification, environmental influences, and functional specificity.<\/p>\n\n\n\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n\n\n\n<p class=\" eplus-wrapper\"><strong>DOI<\/strong>: https:\/\/doi.org\/10.1101\/2024.08.14.607935<\/p>\n\n\n\n<p class=\" eplus-wrapper\"><strong>Keywords<\/strong>: protein structure prediction3D modelsAlphaFold Protein Structure Database (AFDB)ESMAtlasMicrobiome Immunity Project (MIP)structural clusterslow-dimensional representationfunctional profilesbiological functionsopen-access web serverprotein sequence-structure-function relationships<\/p>\n\n\n\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n\n\n\n\t\n    \n        \n\t\t\t<a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.08.14.607935v2\" target=\"_self\"  class=\"button primary \">\n\n\t\t\t\t<span>\n\t\t\t\t\tREAD HERE\n\t\t\t\t<\/span>\n\n\t\t\t<\/a>\n\n        \n    \n","protected":false},"excerpt":{"rendered":"<p>Journal paper in: www.biorxiv.org\/content, 2024<\/p>\n","protected":false},"featured_media":0,"template":"","research_type":[8],"research_team":[113],"class_list":["post-20647","research","type-research","status-publish","hentry","research_type-publications","research_team-structural-and-functional-genomics"],"yoast_head":"<!-- This site is optimized with the Yoast SEO Premium plugin v27.4 (Yoast SEO v27.4) - 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Szydlowski, Witold Wydma\u0144ski, P. Douglas Renfrew, Julia Koehler Leman, Tomasz Kosciolek<\/h2>\n","innerContent":["\n<h2 class=\"wp-block-heading eplus-wrapper\" id=\"h-pawel-szczerbiak-lukasz-m-szydlowski-witold-wydmanski-p-douglas-renfrew-julia-koehler-leman-tomasz-kosciolek\">Pawe\u0142 Szczerbiak, Lukasz M. Szydlowski, Witold Wydma\u0144ski, P. Douglas Renfrew, Julia Koehler Leman, Tomasz Kosciolek<\/h2>\n"]},{"blockName":"core\/spacer","attrs":{"height":"40px","epAnimationGeneratedClass":"edplus_anim-BU3oJP","epGeneratedClass":"eplus-wrapper"},"innerBlocks":[],"innerHTML":"\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n","innerContent":["\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n"]},{"blockName":"core\/paragraph","attrs":{"epAnimationGeneratedClass":"edplus_anim-ydGv10","epGeneratedClass":"eplus-wrapper"},"innerBlocks":[],"innerHTML":"\n<p class=\" eplus-wrapper\">Advances in protein structure prediction have resulted in a remarkable rise in high-quality 3D models, emphasizing the need for effective computational methods to handle and explore this structural data. Our study explores structural clusters derived from the AlphaFold Protein Structure Database (AFDB), a high-quality subset of ESMAtlas, and the Microbiome Immunity Project (MIP). We generate a unified low-dimensional representation of the protein structure space, revealing that while each database occupies distinct regions, they share significant overlap in functional profiles. Key biological functions cluster within specific regions, indicating a common functional landscape across diverse datasets. To support data exploration, we developed an open-access web server. These findings provide a foundation for further research into protein sequence-structure-function relationships, including taxonomic classification, environmental influences, and functional specificity.<\/p>\n","innerContent":["\n<p class=\" eplus-wrapper\">Advances in protein structure prediction have resulted in a remarkable rise in high-quality 3D models, emphasizing the need for effective computational methods to handle and explore this structural data. Our study explores structural clusters derived from the AlphaFold Protein Structure Database (AFDB), a high-quality subset of ESMAtlas, and the Microbiome Immunity Project (MIP). We generate a unified low-dimensional representation of the protein structure space, revealing that while each database occupies distinct regions, they share significant overlap in functional profiles. Key biological functions cluster within specific regions, indicating a common functional landscape across diverse datasets. To support data exploration, we developed an open-access web server. These findings provide a foundation for further research into protein sequence-structure-function relationships, including taxonomic classification, environmental influences, and functional specificity.<\/p>\n"]},{"blockName":"core\/spacer","attrs":{"height":"40px","epAnimationGeneratedClass":"edplus_anim-BU3oJP","epGeneratedClass":"eplus-wrapper"},"innerBlocks":[],"innerHTML":"\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n","innerContent":["\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n"]},{"blockName":"core\/paragraph","attrs":{"epAnimationGeneratedClass":"edplus_anim-b6JXoH","epGeneratedClass":"eplus-wrapper"},"innerBlocks":[],"innerHTML":"\n<p class=\" eplus-wrapper\"><strong>DOI<\/strong>: https:\/\/doi.org\/10.1101\/2024.08.14.607935<\/p>\n","innerContent":["\n<p class=\" eplus-wrapper\"><strong>DOI<\/strong>: https:\/\/doi.org\/10.1101\/2024.08.14.607935<\/p>\n"]},{"blockName":"core\/paragraph","attrs":{"epAnimationGeneratedClass":"edplus_anim-nv0xgb","epGeneratedClass":"eplus-wrapper"},"innerBlocks":[],"innerHTML":"\n<p class=\" eplus-wrapper\"><strong>Keywords<\/strong>: protein structure prediction3D modelsAlphaFold Protein Structure Database (AFDB)ESMAtlasMicrobiome Immunity Project (MIP)structural clusterslow-dimensional representationfunctional profilesbiological functionsopen-access web serverprotein sequence-structure-function relationships<\/p>\n","innerContent":["\n<p class=\" eplus-wrapper\"><strong>Keywords<\/strong>: protein structure prediction3D modelsAlphaFold Protein Structure Database (AFDB)ESMAtlasMicrobiome Immunity Project (MIP)structural clusterslow-dimensional representationfunctional profilesbiological functionsopen-access web serverprotein sequence-structure-function relationships<\/p>\n"]},{"blockName":"core\/spacer","attrs":{"height":"40px","epAnimationGeneratedClass":"edplus_anim-BU3oJP","epGeneratedClass":"eplus-wrapper"},"innerBlocks":[],"innerHTML":"\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n","innerContent":["\n<div style=\"height:40px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n"]},{"blockName":"acf\/button","attrs":{"title":"READ HERE","button_type":"link","url":"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.08.14.607935v2","button_style":"primary","target":"_self","button_extra_classes":""},"innerBlocks":[],"innerHTML":"","innerContent":[]}],"meta_data":{"is_automatically_other_posts":true,"number_of_posts":"3","is_automatically_check_also_posts":true},"_links":{"self":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/research\/20647","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/research"}],"about":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/types\/research"}],"version-history":[{"count":15,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/research\/20647\/revisions"}],"predecessor-version":[{"id":20721,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/research\/20647\/revisions\/20721"}],"wp:attachment":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/media?parent=20647"}],"wp:term":[{"taxonomy":"research_type","embeddable":true,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/research_type?post=20647"},{"taxonomy":"research_team","embeddable":true,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/research_team?post=20647"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}