{"id":13958610,"url":"https://github.com/ohuelab/QEPPI","last_synced_at":"2025-07-21T00:31:24.684Z","repository":{"id":38775165,"uuid":"405635379","full_name":"ohuelab/QEPPI","owner":"ohuelab","description":"Quantitative Estimate Index for Early-Stage Screening of Compounds Targeting Protein-Protein Interactions","archived":false,"fork":false,"pushed_at":"2023-11-28T08:02:05.000Z","size":1607,"stargazers_count":18,"open_issues_count":1,"forks_count":8,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-06-21T07:02:40.064Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ohuelab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-09-12T12:27:01.000Z","updated_at":"2024-10-25T01:01:52.000Z","dependencies_parsed_at":"2024-11-28T02:32:27.511Z","dependency_job_id":"ea4617dd-39ff-4032-8a4b-3cdc2d48c917","html_url":"https://github.com/ohuelab/QEPPI","commit_stats":{"total_commits":1651,"total_committers":3,"mean_commits":550.3333333333334,"dds":0.02967898243488798,"last_synced_commit":"2d3a21eb4f2a2ea4542f193fcfb6de0a379d1caa"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/ohuelab/QEPPI","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ohuelab%2FQEPPI","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ohuelab%2FQEPPI/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ohuelab%2FQEPPI/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ohuelab%2FQEPPI/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ohuelab","download_url":"https://codeload.github.com/ohuelab/QEPPI/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ohuelab%2FQEPPI/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266221262,"owners_count":23894965,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-08-08T13:01:46.365Z","updated_at":"2025-07-21T00:31:19.676Z","avatar_url":"https://github.com/ohuelab.png","language":"Python","readme":"\u003cp align=\"center\"\u003e\n  \u003cimg src=\"https://user-images.githubusercontent.com/7370243/135420088-f616adc8-1e92-4d9b-8b53-0b863497244d.png\"  width=\"400px\"\u003e\n\u003c/p\u003e\n\n# QEPPI\n**Quantitative estimate index for early-stage screening of compounds targeting protein-protein interactions**\n\n[![License](https://img.shields.io/badge/license-MIT-green?style=flat-square)](LICENSE)\n[![GitHub Clones](https://img.shields.io/badge/dynamic/json?style=flat-square?color=success\u0026label=Clones_in_14days\u0026query=count\u0026url=https://github.com/ohuelab/QEPPI/blob/main/clone.json?raw=True\u0026logo=github)](https://github.com/ohuelab/QEPPI/)\n[![Hits](https://hits.seeyoufarm.com/api/count/incr/badge.svg?url=https%3A%2F%2Fgithub.com%2Fohuelab%2FQEPPI\u0026count_bg=%238EC9EE\u0026title_bg=%23555555\u0026icon=\u0026icon_color=%23E7E7E7\u0026title=Hits\u0026edge_flat=true)](https://hits.seeyoufarm.com/)\n![PyPI](https://img.shields.io/pypi/v/QEPPI?style=flat-square)\n[![Python Versions](https://img.shields.io/pypi/pyversions/QEPPI.svg)](https://pypi.org/project/QEPPI/)\n[![tests](https://github.com/ohuelab/QEPPI/actions/workflows/tests.yml/badge.svg)](https://github.com/ohuelab/QEPPI)\n\n## Calculation QEPPI with using Google Colab\nWe have made it so that you can use Google Colab to calculate QEPPI from SMILES without creating your own environment.   \nIf you have a lot of SMILES to calculate, please convert the SMILES to SDF files.  \n\n[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](http://colab.research.google.com/github/ohuelab/QEPPI/blob/main/notebook/QEPPI.ipynb)\n\n## Mininal environment setup (Git clone)\nWe setup it on a Mac (macOS10.15.7), but I'm sure it will run fine on other platforms such as Linux.  \n\n```bash\n# Python 3.7 | 3.8\n# dependencies\npip install rdkit-pypi # \u003e= 2021.3.1.5\npip install numpy      # \u003e= 1.19.5\npip install pandas     # \u003e= 1.1.5\n```\n\nWe also confirmed that QEPPI works with Colab. (see [notebook](https://github.com/ohuelab/QEPPI/blob/main/notebook/QEPPI.ipynb))\n\n### Clone QEPPI\nClone QEPPI repository when you are done with the setup.\n\n```bash\ngit clone https://github.com/ohuelab/QEPPI.git\n```\n\n### Test\nTest it after git clone the QEPPI repository. If the test passes, the QEPPI calculation has been successfully performed. (We used pytest version is 6.2.2)  \n```bash\ncd QEPPI\npytest -v\n```\n\n## QEPPI calculation example\n```bash\n# for .sdf\npython calc_QEPPI.py --sdf PATH_TO_YOUR_COMPOUND.sdf --out PATH_TO_OUTPUT.csv\n```\n```bash\n# for .csv (\"A column name of \"SMILES\" is required.\")\npython calc_QEPPI.py --csv PATH_TO_YOUR_COMPOUND.csv --out PATH_TO_OUTPUT.csv\n```\n\n## Instalation using pip install\nYou can also install QEPPI with ```pip install QEPPI```. The following sample code is available as an implementation example.  \nNote: some dependancies will also be installed with QEPPI module, so a clean environment is preferred!\n```bash\n# QEPPI\npip install QEPPI\n```\n\n```python\nimport QEPPI as ppi\nfrom rdkit import Chem\nfrom rdkit.Chem import SDMolSupplier\n\nq = ppi.QEPPI_Calculator()\nq.read()\n\n# SMILES\nsmiles = \"COC1=CC(=CC=C1NC(=O)[C@@H]1N[C@@H](CC(C)(C)C)[C@@](C#N)([C@H]1C1=CC=CC(Cl)=C1F)C1=CC=C(Cl)C=C1F)C(O)=O\"\nmol = Chem.MolFromSmiles(smiles)\nprint(q.qeppi(mol))\n# 0.7862842663145835\n\n# SDF\nppi_s = SDMolSupplier(\"PATH_TO_SDF/YOUR_COMPOUND.sdf\")\nppi_mols = [mol for mol in ppi_s if mol is not None]\nresult = list(map(q.qeppi, ppi_mols))\n```\n\n## Reference\nIf you find QEPPI useful, please consider citing this publication;\n- Kosugi T, Ohue M. [**Quantitative estimate index for early-stage screening of compounds targeting protein-protein interactions**](https://www.mdpi.com/1422-0067/22/20/10925). _International Journal of Molecular Sciences_, 22(20): 10925, 2021. doi: 10.3390/ijms222010925 \n\nAnother QEPPI publication (conference paper)\n- Kosugi T, Ohue M. [**Quantitative estimate of protein-protein interaction targeting drug-likeness**](https://ieeexplore.ieee.org/abstract/document/9562931/). In _Proceedings of The 18th IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2021)_, 2021. doi: 10.1109/CIBCB49929.2021.9562931 [(PDF)](https://www.li.c.titech.ac.jp/paper/Kosugi-CIBCB2021.pdf) * © 2021 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.\n\n","funding_links":[],"categories":["药物-靶标 药物-药物 化合物-蛋白质 相互作用"],"sub_categories":["网络服务_其他"],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fohuelab%2FQEPPI","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fohuelab%2FQEPPI","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fohuelab%2FQEPPI/lists"}