{"id":1887,"date":"2025-03-05T12:52:30","date_gmt":"2025-03-05T03:52:30","guid":{"rendered":"https:\/\/neuron.catholic.ac.kr\/?p=1887"},"modified":"2025-04-29T16:13:36","modified_gmt":"2025-04-29T07:13:36","slug":"alphafold3-interpretation","status":"publish","type":"post","link":"https:\/\/neuron.catholic.ac.kr\/?p=1887","title":{"rendered":"Alphafold3 interpretation"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">\uad6c\uc870\uc758 \uc815\ud655\ub3c4\ub97c \ud655\uc778\ud558\uae30 \uc704\ud574 \uc2e0\ub8b0\ub3c4 \uc9c0\ud45c\ub97c \ud574\uc11d\ud558\ub294 \ubc29\ubc95<\/h2>\n\n\n\n<p>AF3\uac00 \uc2e4\ud589\ub41c \ud6c4 \ucd9c\ub825\uac12\uc5d0\ub294 \uc2e0\ub8b0\ub3c4 \uc9c0\ud45c(confidence metrics)\uac00 \ud3ec\ud568\ub428.<\/p>\n\n\n\n<h4 class=\"wp-block-heading\"><strong>pLDDT<\/strong> (The Local Di<em>s<\/em>tance Difference Test)<\/h4>\n\n\n\n<p>pLDDT\ub294 0~100 \ubc94\uc704\uc758 \uc6d0\uc790 \ub2e8\uc704 \uc2e0\ub8b0\ub3c4(per-atom confidence)\ub97c \ub098\ud0c0\ub0b4\uba70, \uac12\uc774 \ub192\uc744\uc218\ub85d \uc2e0\ub8b0\ub3c4\uac00 \ub192\uc74c\uc744 \uc758\ubbf8\ud568. \uc774\ub294 \ubcc0\ud615\ub41c LDDT \uc810\uc218\ub97c \uc608\uce21\ud558\ub294 \ub370 \uc0ac\uc6a9\ub418\uba70, \ud3f4\ub9ac\uba38(polymer)\uc640\uc758 \uac70\ub9ac\ub9cc\uc744 \uace0\ub824\ud568.<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>\ub2e8\ubc31\uc9c8\uc758 \uacbd\uc6b0, pLDDT\ub294 <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC3799472\/\" target=\"_blank\" rel=\"noreferrer noopener\">lDDT-C\u03b1 \uc810\uc218<\/a>\uc640 \uc720\uc0ac\ud558\uc9c0\ub9cc, \uc794\uae30(residue) \ub2e8\uc704\uac00 \uc544\ub2cc \uc6d0\uc790(atom) \ub2e8\uc704\ub85c \uc138\ubd84\ud654\ub428.<\/li>\n\n\n\n<li>\ub9ac\uac04\ub4dc(ligand) \uc6d0\uc790\uc758 \uacbd\uc6b0, \ubcc0\ud615\ub41c LDDT\ub294 \ub9ac\uac04\ub4dc \uc6d0\uc790\uc640 \ud3f4\ub9ac\uba38 \uc0ac\uc774\uc758 \uc624\ub958\ub9cc \uace0\ub824\ud558\uba70, \ub2e4\ub978 \ub9ac\uac04\ub4dc \uc6d0\uc790\uc640\uc758 \uc624\ub958\ub294 \ud3ec\ud568\ud558\uc9c0 \uc54a\uc74c.<\/li>\n\n\n\n<li>DNA\/RNA\uc758 \uacbd\uc6b0, \ubcc0\ud615\ub41c LDDT \uacc4\uc0b0\uc5d0 15\u00c5 \ub300\uc2e0 30\u00c5\uc758 \ub354 \ub113\uc740 \ubc18\uacbd\uc774 \uc801\uc6a9\ub428.<br>pLDDT \uac12\uc740 \uad6c\uc870 \uc774\ubbf8\uc9c0\uc5d0\uc11c \uc0c9\uc0c1\uc73c\ub85c \uc2dc\uac01\ud654\ub418\uba70, AlphaFold Database(AFDB)\uc640 \ub3d9\uc77c\ud55c \uc0c9\uc0c1 \ub9e4\ud551\uc774 \uc0ac\uc6a9\ub428.<\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\"><strong>PAE (Predicted Aligned Error, \uc608\uce21 \uc815\ub82c \uc624\ub958)<\/strong><\/h4>\n\n\n\n<p>PAE\ub294 \uc608\uce21\ub41c \uad6c\uc870\uc5d0\uc11c \ub450 \ud1a0\ud070(token) \uac04 \uc0c1\ub300\uc801\uc778 \uc704\uce58 \ubc0f \ubc29\ud5a5 \uc624\ub958\ub97c \ucd94\uc815\ud558\ub294 \uac12.<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>\uac12\uc774 \ub192\uc744\uc218\ub85d \uc608\uce21 \uc624\ub958\uac00 \ud06c\uba70, \ub530\ub77c\uc11c \uc2e0\ub8b0\ub3c4\ub294 \ub0ae\uc544\uc9d0.<\/li>\n\n\n\n<li>\ub2e8\ubc31\uc9c8 \ubc0f \ud575\uc0b0\uc758 \uacbd\uc6b0, PAE \uc810\uc218\ub294 AlphaFold2\uc640 \ub3d9\uc77c\ud558\uba70, \ub2e8\ubc31\uc9c8 \ubc31\ubcf8\uc5d0\uc11c \uc0dd\uc131\ub41c \ud504\ub808\uc784\uc744 \uae30\uc900\uc73c\ub85c \uc624\ub958\ub97c \uce21\uc815\ud568.<\/li>\n\n\n\n<li>\uc18c\ubd84\uc790(small molecules) \ubc0f \ubc88\uc5ed \ud6c4 \ubcc0\ud615(post-translational modifications)\uc758 \uacbd\uc6b0, \uae30\uc900 \uad6c\uc870(reference conformer)\uc5d0\uc11c \uac00\uc7a5 \uac00\uae4c\uc6b4 \uc774\uc6c3 \uc6d0\uc790\ub4e4\uc744 \uc0ac\uc6a9\ud558\uc5ec \uac01 \uc6d0\uc790\uc758 \ud504\ub808\uc784\uc744 \uc0dd\uc131\ud568.<\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\"><strong>pTM \ubc0f ipTM \uc810\uc218<\/strong><\/h4>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>pTM (Predicted Template Modeling) \uc810\uc218<\/strong>\uc640 <strong>ipTM (Interface Predicted Template Modeling) \uc810\uc218<\/strong>\ub294 <strong>TM (Template Modeling) \uc810\uc218<\/strong>\ub97c \uae30\ubc18\uc73c\ub85c \ud568. TM \uc810\uc218\ub294 \uc804\uccb4 \uad6c\uc870\uc758 \uc815\ud655\ub3c4\ub97c \ud3c9\uac00\ud558\ub294 \uc9c0\ud45c\uc784(<a href=\"https:\/\/doi.org\/10.1002\/prot.20264\" target=\"_blank\" rel=\"noreferrer noopener\">Zhang &amp; Skolnick, 2004<\/a>; <a href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btq066\" target=\"_blank\" rel=\"noreferrer noopener\">Xu &amp; Zhang, 2010<\/a>).<\/li>\n\n\n\n<li>pTM \uc810\uc218\uac00 0.5 \uc774\uc0c1\uc774\uba74, \uc608\uce21\ub41c \ubcf5\ud569\uccb4(complex)\uc758 \uc804\ubc18\uc801\uc778 \ud3f4\ub529(fold)\uc774 \uc2e4\uc81c \uad6c\uc870\uc640 \uc720\uc0ac\ud560 \uac00\ub2a5\uc131\uc774 \uc788\uc74c.<\/li>\n\n\n\n<li><strong>ipTM \uc810\uc218<\/strong>\ub294 \ubcf5\ud569\uccb4 \ub0b4 \uc11c\ube0c\uc720\ub2db(subunit) \uac04 \uc0c1\ub300\uc801 \uc704\uce58\uc758 \uc815\ud655\ub3c4\ub97c \uce21\uc815\ud568.\n<ul class=\"wp-block-list\">\n<li><strong>0.8 \uc774\uc0c1<\/strong>: \uc2e0\ub8b0\ud560 \uc218 \uc788\ub294 \uace0\ud488\uc9c8 \uc608\uce21<\/li>\n\n\n\n<li><strong>0.6 \ubbf8\ub9cc<\/strong>: \uc608\uce21 \uc2e4\ud328 \uac00\ub2a5\uc131\uc774 \ub192\uc74c<\/li>\n\n\n\n<li><strong>0.6~0.8 \uc0ac\uc774<\/strong>: \uc608\uce21\uc774 \uc815\ud655\ud560 \uc218\ub3c4 \uc788\uace0 \uc544\ub2d0 \uc218\ub3c4 \uc788\ub294 \ubd88\ud655\uc2e4\ud55c \uc601\uc5ed<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>TM \uc810\uc218\ub294 \uc791\uc740 \uad6c\uc870\ub098 \uc9e7\uc740 \uc11c\uc5f4\uc5d0 \ub300\ud574 \ub9e4\uc6b0 \uc5c4\uaca9\ud558\uae30 \ub54c\ubb38\uc5d0, 20\uac1c \ubbf8\ub9cc\uc758 \ud1a0\ud070\uc774 \ud3ec\ud568\ub41c \uacbd\uc6b0 pTM \uc810\uc218\ub294 <strong>0.05 \ubbf8\ub9cc<\/strong>\uc73c\ub85c \ubd80\uc5ec\ub428. \uc774\ub7ec\ud55c \uacbd\uc6b0 PAE \ub610\ub294 pLDDT\uac00 \uc608\uce21 \ud488\uc9c8\uc744 \ud3c9\uac00\ud558\ub294 \ub370 \ub354 \uc720\uc6a9\ud560 \uc218 \uc788\uc74c.<\/li>\n<\/ul>\n\n\n\n<p>\ubcf4\ub2e4 \uc790\uc138\ud55c \uc2e0\ub8b0\ub3c4 \uc9c0\ud45c\uc5d0 \ub300\ud55c \uc124\uba85\uc740 \ub17c\ubb38\uc5d0\uc11c \ud655\uc778\ud560 \uc218 \uc788\uc74c. \ub610\ud55c, \ub2e8\ubc31\uc9c8 \uad6c\uc131 \uc694\uc18c\uc640 \uad00\ub828\ud558\uc5ec <strong><a href=\"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/alphafold\/inputs-and-outputs\/evaluating-alphafolds-predicted-structures-using-confidence-scores\/\" target=\"_blank\" rel=\"noreferrer noopener\">AlphaFold: A Practical Guide<\/a><\/strong> \uacfc\uc815\uc5d0\uc11c\ub294 \uc2e0\ub8b0\ub3c4 \uc9c0\ud45c\uc5d0 \ub300\ud55c \ucd94\uac00\uc801\uc778 \ud29c\ud1a0\ub9ac\uc5bc\uc744 \uc81c\uacf5\ud568.<\/p>\n\n\n\n<p>\ud2b9\uc815\ud55c \ubd84\uc790(entity) \ub610\ub294 \uc0c1\ud638\uc791\uc6a9(interaction)\uc5d0 \uad00\uc2ec\uc774 \uc788\ub2e4\uba74, \uc804\uccb4 \ubcf5\ud569\uccb4\uac00 \uc544\ub2cc \uac01 \uccb4\uc778(chain) \ub610\ub294 \uccb4\uc778 \uc30d(chain-pair)\uc5d0 \ub300\ud55c \uc2e0\ub8b0\ub3c4 \uac12\uc774 \ub2e4\uc6b4\ub85c\ub4dc \uac00\ub2a5\ud55c \ucd9c\ub825 \ub370\uc774\ud130\uc5d0 \ud3ec\ud568\ub418\uc5b4 \uc788\uc74c. \ubaa8\ub4e0 \uc2e0\ub8b0\ub3c4 \uc9c0\ud45c\uc758 \uc138\ubd80 \uc815\ubcf4\ub294 <strong><a href=\"https:\/\/alphafoldserver.com\/faq#how-do-i-interpret-all-the-outputs-in-the-downloaded-json-files\" target=\"_blank\" rel=\"noreferrer noopener\">JSON \uc139\uc158<\/a><\/strong>\uc5d0\uc11c \ud655\uc778\ud560 \uc218 \uc788\uc74c.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\uad6c\uc870\uc758 \uc815\ud655\ub3c4\ub97c \ud655\uc778\ud558\uae30 \uc704\ud574 \uc2e0\ub8b0\ub3c4 \uc9c0\ud45c\ub97c \ud574\uc11d\ud558\ub294 \ubc29\ubc95 AF3\uac00 \uc2e4\ud589\ub41c \ud6c4 \ucd9c\ub825\uac12\uc5d0\ub294 \uc2e0\ub8b0\ub3c4 \uc9c0\ud45c(confidence metrics)\uac00 \ud3ec\ud568\ub428. pLDDT (The Local Distance Difference Test) pLDDT\ub294 0~100 \ubc94\uc704\uc758 \uc6d0\uc790 \ub2e8\uc704 \uc2e0\ub8b0\ub3c4(per-atom confidence)\ub97c \ub098\ud0c0\ub0b4\uba70, \uac12\uc774 \ub192\uc744\uc218\ub85d \uc2e0\ub8b0\ub3c4\uac00 \ub192\uc74c\uc744 \uc758\ubbf8\ud568. \uc774\ub294 \ubcc0\ud615\ub41c LDDT \uc810\uc218\ub97c \uc608\uce21\ud558\ub294 \ub370 \uc0ac\uc6a9\ub418\uba70, \ud3f4\ub9ac\uba38(polymer)\uc640\uc758 \uac70\ub9ac\ub9cc\uc744 \uace0\ub824\ud568. PAE (Predicted Aligned Error, \uc608\uce21 \uc815\ub82c \uc624\ub958) PAE\ub294 \uc608\uce21\ub41c \uad6c\uc870\uc5d0\uc11c&hellip;&nbsp;<a href=\"https:\/\/neuron.catholic.ac.kr\/?p=1887\" rel=\"bookmark\">\ub354 \ubcf4\uae30 &raquo;<span class=\"screen-reader-text\">Alphafold3 interpretation<\/span><\/a><\/p>\n","protected":false},"author":3,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"neve_meta_sidebar":"","neve_meta_container":"","neve_meta_enable_content_width":"","neve_meta_content_width":0,"neve_meta_title_alignment":"","neve_meta_author_avatar":"","neve_post_elements_order":"","neve_meta_disable_header":"","neve_meta_disable_footer":"","neve_meta_disable_title":"","_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[24,36],"tags":[32,56],"class_list":["post-1887","post","type-post","status-publish","format-standard","hentry","category-ai","category-alphafold","tag-alphafold3","tag-summary-confidence"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.3 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Alphafold3 interpretation - Neuropharm<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/neuron.catholic.ac.kr\/?p=1887\" \/>\n<meta property=\"og:locale\" content=\"ko_KR\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Alphafold3 interpretation - Neuropharm\" \/>\n<meta property=\"og:description\" content=\"\uad6c\uc870\uc758 \uc815\ud655\ub3c4\ub97c \ud655\uc778\ud558\uae30 \uc704\ud574 \uc2e0\ub8b0\ub3c4 \uc9c0\ud45c\ub97c \ud574\uc11d\ud558\ub294 \ubc29\ubc95 AF3\uac00 \uc2e4\ud589\ub41c \ud6c4 \ucd9c\ub825\uac12\uc5d0\ub294 \uc2e0\ub8b0\ub3c4 \uc9c0\ud45c(confidence metrics)\uac00 \ud3ec\ud568\ub428. pLDDT (The Local Distance Difference Test) pLDDT\ub294 0~100 \ubc94\uc704\uc758 \uc6d0\uc790 \ub2e8\uc704 \uc2e0\ub8b0\ub3c4(per-atom confidence)\ub97c \ub098\ud0c0\ub0b4\uba70, \uac12\uc774 \ub192\uc744\uc218\ub85d \uc2e0\ub8b0\ub3c4\uac00 \ub192\uc74c\uc744 \uc758\ubbf8\ud568. \uc774\ub294 \ubcc0\ud615\ub41c LDDT \uc810\uc218\ub97c \uc608\uce21\ud558\ub294 \ub370 \uc0ac\uc6a9\ub418\uba70, \ud3f4\ub9ac\uba38(polymer)\uc640\uc758 \uac70\ub9ac\ub9cc\uc744 \uace0\ub824\ud568. PAE (Predicted Aligned Error, \uc608\uce21 \uc815\ub82c \uc624\ub958) PAE\ub294 \uc608\uce21\ub41c \uad6c\uc870\uc5d0\uc11c&hellip;&nbsp;\ub354 \ubcf4\uae30 &raquo;Alphafold3 interpretation\" \/>\n<meta property=\"og:url\" content=\"https:\/\/neuron.catholic.ac.kr\/?p=1887\" \/>\n<meta property=\"og:site_name\" content=\"Neuropharm\" \/>\n<meta property=\"article:published_time\" content=\"2025-03-05T03:52:30+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2025-04-29T07:13:36+00:00\" \/>\n<meta name=\"author\" content=\"Choi\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"\uae00\uc4f4\uc774\" \/>\n\t<meta name=\"twitter:data1\" content=\"Choi\" \/>\n\t<meta name=\"twitter:label2\" content=\"\uc608\uc0c1 \ub418\ub294 \ud310\ub3c5 \uc2dc\uac04\" \/>\n\t<meta name=\"twitter:data2\" content=\"2\ubd84\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\\\/\\\/neuron.catholic.ac.kr\\\/?p=1887#article\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/neuron.catholic.ac.kr\\\/?p=1887\"},\"author\":{\"name\":\"Choi\",\"@id\":\"https:\\\/\\\/neuron.catholic.ac.kr\\\/#\\\/schema\\\/person\\\/9dd53f622e6bcf6465e81bddfa7ff224\"},\"headline\":\"Alphafold3 interpretation\",\"datePublished\":\"2025-03-05T03:52:30+00:00\",\"dateModified\":\"2025-04-29T07:13:36+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\\\/\\\/neuron.catholic.ac.kr\\\/?p=1887\"},\"wordCount\":82,\"commentCount\":0,\"publisher\":{\"@id\":\"https:\\\/\\\/neuron.catholic.ac.kr\\\/#organization\"},\"keywords\":[\"Alphafold3\",\"Summary confidence\"],\"articleSection\":[\"AI\",\"Alphafold\"],\"inLanguage\":\"ko-KR\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\\\/\\\/neuron.catholic.ac.kr\\\/?p=1887#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/neuron.catholic.ac.kr\\\/?p=1887\",\"url\":\"https:\\\/\\\/neuron.catholic.ac.kr\\\/?p=1887\",\"name\":\"Alphafold3 interpretation - 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