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PUNCH2

A residue-level Intrinsically Disordered Region/Protein(IDP/IDR) predictor trained on PDB and Disprot Databases.

\n\n## 📝 Description\nPUNCH2 project belongs to a serious of PUNCH projects which focus on the Structure and Function prediction of Intrisically Diordered Protein/Region (IDP/IDR).\nCurrently we have PUNCH2 for IDR structure prediction, and PUNCH_Linker and PUNCH_Linker_Light for DFL prediction. \n\n## 🐣 Getting Started\nCurrently, we provide two ways to use this perdictor: Docker or Download source code from this Github.\n### Pre-requirements\nThis predictor requires sequences embedded with ONEHOT, [ProtTrans](https://github.com/agemagician/ProtTrans), and [MSA Transformer](https://github.com/facebookresearch/esm).\n\nNote, \n* File format should be `[SEQUENCE_NAME/ID].npy`, replace *SEQUENCE_NAME/ID* with the actural sequence ID, it should be the same as the name from `.fasta` file.\n* Matrix shape: \\\n **Onehot**: (1, 227, 21) \\\n **ProtTrans**: (1, 227, 1024) \\\n **MSA Transformer**: (1, 227, 768)\n\n📣‼️If you don't have them available, please visit the **[embedding](https://github.com/deemeng/embedding)** section of our project first to embed the sequences.‼️\n\n(We maintain this separation due to the requirements from [CAID3](https://caid.idpcentral.org/challenge), but we may edit or merge them in the future.)\n### Docker\n#### Dependencies\n* Onehot, [ProtTrans](https://github.com/agemagician/ProtTrans), and [MSA Transformer](https://github.com/facebookresearch/esm) embedded sequences;\n* Docker Desktop 4.27.2 or higher;\n#### Installing\n* Pull the Docker image from DockerHub\n ```sh\n docker pull dimeng851/punch2:v1\n ```\n\n#### Executing program\n* RUN the following command:\n >Replace \\\n >`CONTAINER_NAME` - anyname you like; \\\n >`PATH_TO_INPUT_FASTA` - path to input file, which is **ONE** FASTA file including all query sequences; \\\n >`PATH_TO_ONEHOT` - a folder which includes all ONEHOT embedded sequences; \\\n >`PATH_TO_MSATRANS` - a folder which includes all MSA Transformer embedded sequences; \\\n >`PATH_TO_PROTTRANS` - a folder which includes all protTrans embedded sequences; \\\n >`PATH_OUTPUT` - a folder which will be used to save all outputs, including: a. timings.csv; b. disorder folder, where will keep all the prediction resulds.\n ```sh\n docker run -d \\\n -it \\\n --name [CONTAINER_NAME] \\\n --mount type=bind,source=[PATH_TO_INPUT_FASTA],target=/punch2/data/input.fasta \\\n --mount type=bind,source=[PATH_TO_ONEHOT],target=/punch2/data/onehot \\\n --mount type=bind,source=[PATH_TO_MSATRANS],target=/punch2/data/msaTrans \\\n --mount type=bind,source=[PATH_TO_PROTTRANS],target=/punch2/data/protTrans \\\n --mount type=bind,source=[PATH_OUTPUT],target=/punch2/output \\\n dimeng851/punch2:v1\n ```\n > \n >An example:\n ```sh\n docker run -d \\\n -it \\\n --name punch2_con \\\n --mount type=bind,source=/home/dimeng/caid3/test_idr.fasta,target=/punch2/data/input.fasta \\\n --mount type=bind,source=/home/dimeng/project/idr/data/caid/features/onehot,target=/punch2/data/onehot \\\n --mount type=bind,source=/home/dimeng/project/idr/data/caid/features/msaTrans,target=/punch2/data/msaTrans \\\n --mount type=bind,source=/home/dimeng/project/idr/data/caid/features/protTrans,target=/punch2/data/protTrans \\\n --mount type=bind,source=/home/dimeng/caid3/punch_idr_output,target=/punch2/output \\\n dimeng851/punch2:v1\n ```\n* Find the results in **OUTPUT** folder.\n\n## Contact & Help 📩\n\nEmail Di.\n```\ndi.meng@ucdconnect.ie\n```\n\n## Authors\n📬 Di Meng - di.meng@ucdconnect.ie \\\n📬 Gianluca Pollastri - gianluca.pollastri@ucd.ie\n\n## Project\n>https://github.com/deemeng/punch2","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",2968521131,"orgData","recentTags",[91],{"_92":44,"_93":94,"_95":96,"_97":98,"_99":100,"_101":102,"_50":117,"_118":94,"_119":33,"_120":56,"_57":121,"_122":123,"_124":108,"_125":117,"_126":66,"_127":21},"content_type","creator",25366396,"digest","sha256:e8f846abab9fb02fe7387bd89465c8f250341f12996d4bcaff280641b067445b","full_size",2968511585,"id",639045607,"images",[103],{"_104":105,"_95":96,"_106":48,"_107":108,"_109":110,"_111":112,"_113":48,"_114":-5,"_115":98,"_63":66,"_116":-5},"architecture","amd64","features","last_pulled","2026-10-05T12:13:14.444638569Z","last_pushed","2024-04-12T11:02:51Z","os","linux","os_features","os_version","size","variant","2024-04-12T11:02:50.468Z","last_updater","last_updater_username","media_type","v1","repository",23811349,"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":141,"_148":149,"_135":158,"_159":11},{"_40":142,"_42":143,"_45":46,"_47":48,"_49":11,"_50":51,"_52":53,"_54":144,"_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":145,"_79":11,"_80":147,"_85":33,"_86":87},[],[44],[56],{"_75":11,"_76":146},[78],{"_82":21,"_83":11,"_84":11},"tags",{"_150":64,"_151":-5,"_152":-5,"_153":154},"count","next","previous","results",[155],{"_92":44,"_93":94,"_95":96,"_97":98,"_99":100,"_101":156,"_50":117,"_118":94,"_119":33,"_120":56,"_57":121,"_122":123,"_124":108,"_125":117,"_126":66,"_127":21},[157],{"_104":105,"_95":96,"_106":48,"_107":108,"_109":110,"_111":112,"_113":48,"_114":-5,"_115":98,"_63":66,"_116":-5},[],"canDeleteTags","actionData","errors"]

dimeng851/punch2

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