[{"_1":2,"_161":-5,"_162":-5},"loaderData",{"_3":4,"_17":18,"_25":26,"_140":141},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7,"_13":14,"_15":16},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","theme","system","contrast","normal","routes/_layout",{"_19":-5,"_20":21,"_22":21,"_23":11,"_24":21},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_27":28,"_29":-5,"_30":11,"_31":11,"_32":33,"_34":35,"_36":-5,"_37":11,"_38":39,"_88":-5,"_89":90,"_129":-5,"_130":11,"_131":21,"_132":11,"_133":-5,"_134":11,"_135":-5,"_136":137,"_138":91,"_139":-7},"canonicalUrl","https://hub.docker.com/r/jongseopark/oligofold/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","jongseopark","reponame","oligofold","cloudBuildSource","isAutobuildsAvailable","repo",{"_40":41,"_42":43,"_45":46,"_47":48,"_49":11,"_50":51,"_52":53,"_54":55,"_57":35,"_32":33,"_58":59,"_60":44,"_61":62,"_63":64,"_65":66,"_67":-5,"_68":62,"_69":70,"_71":11,"_72":33,"_73":74,"_79":11,"_80":81,"_85":33,"_86":87},"categories",[],"content_types",[44],"image","date_registered","2021-08-30T04:17:45.891501Z","description","The docker image comprising AlphaFold 2 with modified code for multimer modeling.","is_private","last_updated","2021-08-30T04:24:18.876722Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[56],"application/vnd.docker.container.image.v1+json","name","pull_count",196,"repository_type","star_count",0,"status",1,"status_description","active","source","collaborator_count","full_description","# ***[OligoFold] AlphaFold_oligomer***\n\n\n
\n\n*[Link to related GitHub page](https://github.com/jongseo-park/AlphaFold_oligomer)*\n\n
\n\n\nThis repository has several scripts that enables **oligomer modeling** using DeepMind's AlphaFold.\n\n\nYou can model a oligomeric structure comprising up to three types of sequences, with any number of protomers.\n\n*[DeepMind's AlphaFold](https://github.com/deepmind/alphafold)*\n\n\n
\n\nThese scripts were developed based on the codes of AlphaFold Colab ([community version](https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb)) made by Dr. Martin Steinegger, Sergey Ovchinnikov, and Milot Mirdita \$with the insights of Dr. Minkyoung Baek *(RoseTTAFold)* and Yoshitaka Moriwaki\$, which uses API hosted at the Södinglab based on the MMseqs2 server.\n\n*[ColabFold GitHub](https://github.com/sokrypton/ColabFold)*\n\n\n
\n\nThese scripts are designed to work in the system which already has a installed AlphaFold.\n\nYou can also use a already prepared docker image of this ***OligoFold***, but it may not work if the system environment is different.\n\nPlease refer the description at the bottom.\n\n\n
\n \n- - -\n\n
\n\n이 저장소에서는 구글 딥마인드의 알파폴드를 통한 oligomeric structure 모델링을 가능케하는 코드를 공유합니다.\n\n총 세 종류의 단백질 시퀀스를 이용할 수 있고, protomer 의 수를 설정하는 것에는 제한이 없습니다.\n\n
\n\n이 저장소에 있는 스크립트들은 알파폴드 Colab ([community version](https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb)) 에 있는 코드에 기반하여 제작되었습니다.\n\n스크립트 사용을 위해서는 이미 알파폴드를 설치 및 실행할 수 있는 시스템 환경이 필요합니다.\n\n
\n\n사용법은 아래와 같습니다.\n\n
\n\n## ***How to use***\n\n### 1. Set the path for database and result\n\nOpen the **\\[run_docker_oligofold.py\\]** using text editor, and modify ***line 31 and 37*** to be the path to the directory containing the databases and result folder, respectively.\n\n line 31: DOWNLOAD_DIR = '/path/to/database'\n line 37: output_dir = '/path/to/your/result'\n\n
\n\n### 2. Copy and paste those scripts\n\n pipeline.py >> /alphafold/alphafold/data/\n run_alphafold.py >> /alphafold/\n run_docker_oligofold.py >> /alphafold/docker/\n\n
\n\n### 3. Rebuild the docker image\n\nRebuild the docker image using the Dockerfile already used to install the AlphaFold. At this point, the name of the image is named *\\'oligofold\\'*.\n\n cd /alphafold/\n docker build -f docker/Dockerfile -t oligofold . \n\n
\n \n### 4. Run\n\nRunning protocol of the oligofold is almost identical with that of the original AlphaFold, but there are several differences.\n\nYou have to set the path of one essential fasta file using the argument, ***\\'--fasta_paths\\'***.\n\nYou can set the number of protomers of the essential fasta file using the argument, ***\\'--oligo1\\'***.\n\nSince the default number of ***\\'oligo1\\'*** is 1, it is not necessary to set a value, but if you want to make homooligomer using that fasta file, just set the number of it.\n\n
\n\nOptionally, you can set up the other two fasta paths using these arguments, ***\\'--fasta2_paths\\'*** and ***\\'--fasta3_paths\\'***.\n\nYou are also able to set up the number of protomers you want for the fasta2 and fasta3 using these arguments, ***\\'--oligo2\\'*** and ***\\'--oligo3\\'***, respectively.\n\nIf you don't want to use the other fasta files, just ignore these options.\n\n
\n \nFinally, you are also able to choose whether to do the amber relaxation or not, using the argument, ***\\'--amberrelax\\'*** *(y/n)*.\n\nThis is an example command.\n\n python3 docker/run_docker_oligofold.py\n --fasta_paths=/path/to/first/fastafile\n --fasta2_paths=/path/to/second/fastafile\n --max_template_date=2021-07-31\n --preset=reduced_dbs\n --oligo1=2\n --oligo2=1\n --amberrelax=n\n\nThen, the modelled structure comprising two identical molecules and one another molecule will be obtained.\n\n
\n\nIf you want to model the complex structure comprising three types of proteins, \n\njust enter the three sequences and the number of protomers of each.\n\n python3 docker/run_docker_oligofold.py\n --fasta_paths=/path/to/first/fastafile\n --fasta2_paths=/path/to/second/fastafile\n --fasta3_paths=/path/to/third/fastafild\n --max_template_date=2021-07-31\n --preset=reduced_dbs\n --oligo1=2\n --oligo2=1\n --oligo3=2\n --amberrelax=n\n\n\n
\n
\n\n- - -\n## ***Already prepared docker image***\n\nThe already prepared docker image may not work due to the differences of system environment. \n\nThis is my system environment\n\n Ubuntu 20.04\n i9-10900x\n 128 GB RAM\n RTX 3080 * 2 ea\n CUDA version 11.2\n NVIDIA driver version 460.27.04\n\n\n
\n\nNeverthelss, if you want to try this ...\n\nYou can download the docker image as follows.\n\n docker pull jongseopark/oligofold\n\n
\n\nAnd then, change the name of docker image from **jongseopark/oligofold:latest** to **oligofold:latest**\n\n docker tag jongseopark/oligofold:latest oligofold:latest\n\n
\n\nOpen the **\\[run_docker_oligofold.py\\]** using text editor, and modify ***line 31 and 37*** to be the path to the directory containing the databases and result folder, respectively.\n\n line 31: DOWNLOAD_DIR = '/path/to/database'\n line 37: output_dir = '/path/to/your/result'\n\n
\n\nThere is no need to rebuild the docker image, because you already download it.\n\nJust type the running command as described earlier.\n\n\n- - -\n\n## ***And ...***\n\nSince I am a structural biologist, but not a computational biologist, those scripts which I wrote might not be fancy or cause error. So, feel free to contact me, and tell or teach about the coding.\n\n
\n
\n\n*Thanks.*\n","has_starred","hub_user","immutable_tags_settings",{"_75":11,"_76":77},"enabled","rules",[78],".*","is_automated","permissions",{"_82":21,"_83":11,"_84":11},"read","write","admin","user","storage_size",6503176181,"orgData","recentTags",[91],{"_92":44,"_93":94,"_95":96,"_97":98,"_99":100,"_50":118,"_119":94,"_120":33,"_121":56,"_57":122,"_123":124,"_125":109,"_126":118,"_127":66,"_128":21},"content_type","creator",10703569,"full_size",6503157586,"id",164878980,"images",[101],{"_102":103,"_104":105,"_106":107,"_108":109,"_110":111,"_112":113,"_114":107,"_115":-5,"_116":96,"_63":66,"_117":-5},"architecture","amd64","digest","sha256:be21d46112ba3445433852beb29e6086780c5c3f361f0600cd66a3f325afe5a4","features","","last_pulled","2026-09-27T02:54:30.9254277Z","last_pushed","2021-08-30T04:24:19Z","os","linux","os_features","os_version","size","variant","2021-08-30T04:24:18.404334Z","last_updater","last_updater_username","media_type","latest","repository",15251331,"tag_last_pulled","tag_last_pushed","tag_status","v2","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","showSbxLogoOverride","sbxTrademarkText","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"selectedTag","attestationsUrl","routes/_layout.r.$namespace.$reponame.tags",{"_38":142,"_149":150,"_136":159,"_160":11},{"_40":143,"_42":144,"_45":46,"_47":48,"_49":11,"_50":51,"_52":53,"_54":145,"_57":35,"_32":33,"_58":59,"_60":44,"_61":62,"_63":64,"_65":66,"_67":-5,"_68":62,"_69":70,"_71":11,"_72":33,"_73":146,"_79":11,"_80":148,"_85":33,"_86":87},[],[44],[56],{"_75":11,"_76":147},[78],{"_82":21,"_83":11,"_84":11},"tags",{"_151":64,"_152":-5,"_153":-5,"_154":155},"count","next","previous","results",[156],{"_92":44,"_93":94,"_95":96,"_97":98,"_99":157,"_50":118,"_119":94,"_120":33,"_121":56,"_57":122,"_123":124,"_125":109,"_126":118,"_127":66,"_128":21},[158],{"_102":103,"_104":105,"_106":107,"_108":109,"_110":111,"_112":113,"_114":107,"_115":-5,"_116":96,"_63":66,"_117":-5},[],"canDeleteTags","actionData","errors"]

jongseopark/oligofold

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