{ "_id": "6a17e0daacfb0bcc41d9eeff", "Package": "DeepPINCS", "Type": "Package", "Title": "Protein Interactions and Networks with Compounds based on\nSequences using Deep Learning", "Description": "The identification of novel compound-protein interaction\n(CPI) is important in drug discovery. Revealing unknown\ncompound-protein interactions is useful to design a new drug\nfor a target protein by screening candidate compounds. The\naccurate CPI prediction assists in effective drug discovery\nprocess. To identify potential CPI effectively, prediction\nmethods based on machine learning and deep learning have been\ndeveloped. Data for sequences are provided as discrete symbolic\ndata. In the data, compounds are represented as SMILES\n(simplified molecular-input line-entry system) strings and\nproteins are sequences in which the characters are amino acids.\nThe outcome is defined as a variable that indicates how strong\ntwo molecules interact with each other or whether there is an\ninteraction between them. In this package, a deep-learning\nbased model that takes only sequence information of both\ncompounds and proteins as input and the outcome as output is\nused to predict CPI. The model is implemented by using compound\nand protein encoders with useful features. The CPI model also\nsupports other modeling tasks, including protein-protein\ninteraction (PPI), chemical-chemical interaction (CCI), or\nsingle compounds and proteins. Although the model is designed\nfor proteins, DNA and RNA can be used if they are represented\nas sequences.", "Version": "1.21.0", "Date": "2023-07-06", "Authors@R": "c(person(given=\"Dongmin\", family=\"Jung\", email=\"dmdmjung@gmail.com\", role=c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0001-7499-8422\")))", "LazyData": "TRUE", "LazyDataCompression": "xz", "License": "Artistic-2.0", "biocViews": "Software, Network, GraphAndNetwork, NeuralNetwork", "NeedsCompilation": "no", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake libglpk-dev make default-jdk libicu-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev python3 libx11-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:55:56 UTC", "RemoteUrl": "https://github.com/bioc/DeepPINCS", "RemoteRef": "HEAD", "RemoteSha": "e597bf45b0a29141c76bb6fc439e65dfdb329ecb", "Packaged": { "Date": "2026-05-28 06:24:19 UTC", "User": "root" }, "Author": "Dongmin Jung [cre, aut] (ORCID:\n)", "Maintainer": 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version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380956 }, "_maintainer": { "name": "Dongmin Jung", "email": "dmdmjung@gmail.com", "login": "dongminjung", "description": "", "uuid": 25045090, "orcid": "0000-0001-7499-8422" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "keras", "role": "Depends" }, { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "tensorflow", "role": "Imports" }, { "package": "CatEncoders", "role": "Imports" }, { "package": "matlab", "role": "Imports" }, { "package": "rcdk", "role": "Imports" }, { "package": "stringdist", "role": "Imports" }, { "package": "tokenizers", "role": "Imports" }, { "package": "webchem", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "ttgsea", "role": "Imports" }, { "package": "PRROC", "role": "Imports" }, { "package": "reticulate", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "knitr", "role": "Suggests" 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