{"id":4078,"date":"2025-04-02T01:13:40","date_gmt":"2025-04-01T16:13:40","guid":{"rendered":"https:\/\/bdsl.jbnu.ac.kr\/blog\/?p=4078"},"modified":"2025-04-02T01:36:12","modified_gmt":"2025-04-01T16:36:12","slug":"protein-structure-modeling-with-colabfold-alphafold2","status":"publish","type":"post","link":"https:\/\/bdsl.jbnu.ac.kr\/blog\/protein-structure-modeling-with-colabfold-alphafold2\/","title":{"rendered":"Protein Structure Modeling with ColabFold &#8211; AlphaFold2"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">Introduction <\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">ColabFold\ub294 Google Colab \ud658\uacbd\uc5d0\uc11c AlphaFold2\ub97c \uc218\ud589\ud560 \uc218 \uc788\ub294 \uae30\ub2a5\uc744 \uc81c\uacf5\ud55c\ub2e4. Google \uacc4\uc815\uc774 \uc788\uc73c\uba74 \uc6f9 \ube0c\ub77c\uc6b0\uc838\ub97c \ud1b5\ud574 \uc811\uadfc\ud558\uc5ec \ub2e8\ubc31\uc9c8 \uad6c\uc870 \ubaa8\ub378\ub9c1\uc744 \uc218\ud589\ud560 \uc218 \uc788\ub2e4. \uc5ec\uae30\uc11c\ub294 ColabFold\ub97c \uc774\uc6a9\ud574 \ub2e8\ubc31\uc9c8 \uc11c\uc5f4\uc744 \uc774\uc6a9\ud574 \uad6c\uc870\ub97c \uc608\uce21\ud558\ub294 \uc2e4\uc2b5\uc744 \uc2e4\ud589\ud558\uace0, \uc0dd\uc131\ub41c \ud30c\uc77c\uc744 \ubd84\uc11d\ud569\ub2c8\ub2e4.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n\n\n\n<h2 class=\"wp-block-heading\">ColabFold<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">1. \uc811\uc18d<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">ColabFold\ub294 \uc544\ub798 link\ub97c \ud1b5\ud574 \uc811\uc18d\ud569\ub2c8\ub2e4. <\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Google Colab &#8211; AlphaFold2 by \n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/colab.research.google.com\/github\/sokrypton\/ColabFold\/blob\/main\/AlphaFold2.ipynb\">https:\/\/colab.research.google.com\/github\/sokrypton\/ColabFold\/blob\/main\/AlphaFold2.ipynb<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">\uc544\ub798\uc640 \uac19\uc740 JupyterNotebook \ud654\uba74\uc744 \ud655\uc778\ud560 \uc218 \uc788\uc2b5\ub2c8\ub2e4. <\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"477\" src=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/04\/image-1024x477.png\" alt=\"\" class=\"wp-image-4079\" srcset=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/04\/image-1024x477.png 1024w, https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/04\/image-300x140.png 300w, https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/04\/image-768x358.png 768w, https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/04\/image-1536x715.png 1536w, https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/04\/image-2048x954.png 2048w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<h3 class=\"wp-block-heading\">2. \uc11c\uc5f4 \uc785\ub825<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\"> <code>query_sequence<\/code> \uc606 \uce78\uc5d0 \uad6c\uc870\ub97c \uc608\uce21\ud560 \ub2e8\ubc31\uc9c8\uc758 \uc11c\uc5f4\uc744 \uc785\ub825\ud569\ub2c8\ub2e4. <\/p>\n\n\n\n<h3 class=\"wp-block-heading\">3. \uad6c\uc870 \ubaa8\ub378\ub9c1 <\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>&#8220;\ub7f0\ud0c0\uc784(Runtime)&#8221; > &#8220;\ubaa8\ub450 \uc2e4\ud589(Run All )&#8221;\uc744 \uc2e4\ud589\ud569\ub2c8\ub2e4. <\/li>\n\n\n\n<li>\uad6c\uc870 \ubaa8\ub378\ub9c1\uc774 \uc2dc\uc791\ub418\uace0, \ub2e8\ubc31\uc9c8 \uad6c\uc870 \uc608\uce21\uc774 \uc9c4\ud589\ub429\ub2c8\ub2e4. <\/li>\n\n\n\n<li>\ucd5c\uc885 \uc0dd\uc131 \ud30c\uc77c (.zip) \ud30c\uc77c\uc774 \uc0dd\uc131\ub418\uba74 \uacb0\uacfc\ub97c \ubc1b\uc744 \uc218 \uc788\uc2b5\ub2c8\ub2e4.<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n\n\n\n<h3 class=\"wp-block-heading\">4. \uacb0\uacfc <\/h3>\n\n\n\n<h4 class=\"wp-block-heading\">4.1. Multiple Sequence Alignment <\/h4>\n\n\n\n<ul class=\"wp-block-list\">\n<li>\uc9c4\ud654\ud558\uc801\uc73c\ub85c \uc5f0\uad00\ub41c \uc11c\uc5f4 <\/li>\n<\/ul>\n\n\n\n<figure class=\"wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"1012\" height=\"678\" src=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/04\/image-1.png\" alt=\"\" class=\"wp-image-4082\" srcset=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/04\/image-1.png 1012w, https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/04\/image-1-300x201.png 300w, https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/04\/image-1-768x515.png 768w\" sizes=\"auto, (max-width: 1012px) 100vw, 1012px\" \/><\/figure>\n\n\n\n<h4 class=\"wp-block-heading\">4.2 Model \uc0dd\uc131 <\/h4>\n\n\n\n<ul class=\"wp-block-list\">\n<li>\uc608\uce21 \uad6c\uc870 \uc0dd\uc131 (5\uac1c \uad6c\uc870 \uc0dd\uc131)<\/li>\n<\/ul>\n\n\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"639\" src=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/04\/image-2-1024x639.png\" alt=\"\" class=\"wp-image-4083\" srcset=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/04\/image-2-1024x639.png 1024w, https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/04\/image-2-300x187.png 300w, https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/04\/image-2-768x480.png 768w, https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/04\/image-2.png 1270w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<h4 class=\"wp-block-heading\">4.3. \uad6c\uc870 \ubaa8\ub378 \ud3c9\uac00 <\/h4>\n\n\n\n<ul class=\"wp-block-list\">\n<li> pLDDT (predicted Local Distance Difference Test): residue\ubcc4 \uc704\uce58 \uc815\ud655\ub3c4 (\uc608\uce21\uce58)\n<ul class=\"wp-block-list\">\n<li>> 90: \ub192\uc740 \uc2e0\ub8b0\ub3c4 <\/li>\n\n\n\n<li>70-90: \uc2e0\ub8b0\ud560 \ub9cc\ud55c \uad6c\uc870 \uc608\uce21<\/li>\n\n\n\n<li>50-70: \ub0ae\uc740 \uc2e0\ub8b0\ub3c4 \uad6c\uac04<\/li>\n\n\n\n<li>&lt;50: \uba85\ud655\ud55c \uad6c\uc870\uac00 \uc874\uc7ac\ud558\uc9c0 \uc54a\ub294 \uad6c\uac04 <\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>pTM (predicted TM score): \uc804\uccb4 \uad6c\uc870(fold)\uc758 \uc2e0\ub8b0\ub3c4\n<ul class=\"wp-block-list\">\n<li>> 0.7: \uc804\uccb4 \uad6c\uc870(fold)\uac00 \uc77c\uce58\ud560 \uac00\ub2a5\uc131\uc774 \ub192\uc74c<\/li>\n\n\n\n<li>&lt;0.5: \uc804\uccb4 \uad6c\uc870\uac00 \uc815\ud655\ud558\uc9c0 \uc54a\uc744 \uac00\ub2a5\uc131\uc774 \uc788\uc74c<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>pIDDT (predicted Inter-residue Distance Difference Test): complex \uad6c\uc870\uc758 chain \uac04 \uad6c\uc870 \uc815\ud655\ub3c4 (AlphaFold-Multimer)<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Introduction ColabFold\ub294 Google Colab \ud658\uacbd\uc5d0\uc11c AlphaFold2\ub97c \uc218\ud589\ud560 \uc218 \uc788\ub294 \uae30\ub2a5\uc744 \uc81c\uacf5\ud55c\ub2e4. Google \uacc4\uc815\uc774 \uc788\uc73c\uba74 \uc6f9 \ube0c\ub77c\uc6b0\uc838\ub97c \ud1b5\ud574 \uc811\uadfc\ud558\uc5ec \ub2e8\ubc31\uc9c8 \uad6c\uc870 \ubaa8\ub378\ub9c1\uc744 \uc218\ud589\ud560 \uc218 \uc788\ub2e4. \uc5ec\uae30\uc11c\ub294 ColabFold\ub97c \uc774\uc6a9\ud574 \ub2e8\ubc31\uc9c8 \uc11c\uc5f4\uc744 \uc774\uc6a9\ud574 \uad6c\uc870\ub97c \uc608\uce21\ud558\ub294 \uc2e4\uc2b5\uc744 \uc2e4\ud589\ud558\uace0, \uc0dd\uc131\ub41c \ud30c\uc77c\uc744 \ubd84\uc11d\ud569\ub2c8\ub2e4. ColabFold 1. \uc811\uc18d ColabFold\ub294 \uc544\ub798 link\ub97c \ud1b5\ud574 \uc811\uc18d\ud569\ub2c8\ub2e4. \uc544\ub798\uc640 \uac19\uc740 JupyterNotebook \ud654\uba74\uc744 \ud655\uc778\ud560 \uc218 \uc788\uc2b5\ub2c8\ub2e4. 2. \uc11c\uc5f4 \uc785\ub825 [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_uag_custom_page_level_css":"","site-sidebar-layout":"default","site-content-layout":"","ast-site-content-layout":"default","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","ast-disable-related-posts":"","theme-transparent-header-meta":"","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"set","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"ast-content-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"footnotes":"","_members_access_role":[],"_members_access_error":""},"categories":[48],"tags":[],"class_list":["post-4078","post","type-post","status-publish","format-standard","hentry","category-computation-biochemistry"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v28.4 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Protein Structure Modeling with ColabFold - AlphaFold2 - Biomedical Data Science Laboratory<\/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:\/\/bdsl.jbnu.ac.kr\/blog\/protein-structure-modeling-with-colabfold-alphafold2\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Protein Structure Modeling with ColabFold - AlphaFold2 - Biomedical Data Science Laboratory\" \/>\n<meta property=\"og:description\" content=\"Introduction ColabFold\ub294 Google Colab \ud658\uacbd\uc5d0\uc11c AlphaFold2\ub97c \uc218\ud589\ud560 \uc218 \uc788\ub294 \uae30\ub2a5\uc744 \uc81c\uacf5\ud55c\ub2e4. Google \uacc4\uc815\uc774 \uc788\uc73c\uba74 \uc6f9 \ube0c\ub77c\uc6b0\uc838\ub97c \ud1b5\ud574 \uc811\uadfc\ud558\uc5ec \ub2e8\ubc31\uc9c8 \uad6c\uc870 \ubaa8\ub378\ub9c1\uc744 \uc218\ud589\ud560 \uc218 \uc788\ub2e4. \uc5ec\uae30\uc11c\ub294 ColabFold\ub97c \uc774\uc6a9\ud574 \ub2e8\ubc31\uc9c8 \uc11c\uc5f4\uc744 \uc774\uc6a9\ud574 \uad6c\uc870\ub97c \uc608\uce21\ud558\ub294 \uc2e4\uc2b5\uc744 \uc2e4\ud589\ud558\uace0, \uc0dd\uc131\ub41c \ud30c\uc77c\uc744 \ubd84\uc11d\ud569\ub2c8\ub2e4. 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