{"id":20995181,"url":"https://github.com/seonghwanseo/openpharmaco","last_synced_at":"2025-05-14T21:31:07.020Z","repository":{"id":243596499,"uuid":"794819876","full_name":"SeonghwanSeo/OpenPharmaco","owner":"SeonghwanSeo","description":"Open-source protein-based pharmacophore modeling software","archived":false,"fork":false,"pushed_at":"2025-02-15T07:04:09.000Z","size":25841,"stargazers_count":21,"open_issues_count":2,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-04-02T23:41:32.754Z","etag":null,"topics":["deep-learning","drug-discovery","machine-learning","pharmacophore-modelling","protein-based-pharmacophore-modelling","virtual-screening"],"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/SeonghwanSeo.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":"2024-05-02T02:44:43.000Z","updated_at":"2025-02-15T07:04:01.000Z","dependencies_parsed_at":"2024-06-10T04:23:22.000Z","dependency_job_id":"2363df9d-169d-429a-b1db-ad22ebc0d791","html_url":"https://github.com/SeonghwanSeo/OpenPharmaco","commit_stats":null,"previous_names":["seonghwanseo/openpharmaco"],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SeonghwanSeo%2FOpenPharmaco","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SeonghwanSeo%2FOpenPharmaco/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SeonghwanSeo%2FOpenPharmaco/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SeonghwanSeo%2FOpenPharmaco/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/SeonghwanSeo","download_url":"https://codeload.github.com/SeonghwanSeo/OpenPharmaco/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254230825,"owners_count":22036250,"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":["deep-learning","drug-discovery","machine-learning","pharmacophore-modelling","protein-based-pharmacophore-modelling","virtual-screening"],"created_at":"2024-11-19T07:22:17.820Z","updated_at":"2025-05-14T21:31:01.976Z","avatar_url":"https://github.com/SeonghwanSeo.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# OpenPharmaco: Open-source Protein-based Pharmacophore Modeling Software\n\n \u003cimg src=\"images/logo.png\" alt=\"OpenPharmaco Logo\" height=\"160\"\u003e\n\nOpen-Source software for Fully-automated Protein-based Pharmacophore Modeling and High-throughput Virtual Screening.\n\nOpenPharmaco is currently powered by ***PharmacoNet: Accelerating Large-Scale Virtual Screening by Deep Pharmacophore Modeling***, developed by Seonghwan Seo, KAIST.\n\nIf you are deep learning researcher, please visit PharmacoNet [[github](https://github.com/SeonghwanSeo/PharmacoNet)]. It provides more functions.\n\nIf you have any problems or need help, please add an github issue.\n\nYou can get more information at [Wiki](https://github.com/SeonghwanSeo/OpenPharmaco/wiki).\n\n\\* Tested on Microsoft Window and Mac OS X (Apple Silicon).\n\n\n\n## Quick Start\n\n```bash\n# Download Source Codes\ngit clone https://github.com/SeonghwanSeo/OpenPharmaco.git\n\n# Create Environment\ncd OpenPharmaco/\nconda env create -f environment.yml\nconda activate openph\npip install .\n\n# Start\nconda activate openph\nopenph # or openpharmaco\n```\n\n\n\n## Citation\n\nPaper on [arxiv](https://arxiv.org/abs/2310.00681)\n\n```\n@article{seo2023pharmaconet,\n  title = {PharmacoNet: Accelerating Large-Scale Virtual Screening by Deep Pharmacophore Modeling},\n  author = {Seo, Seonghwan and Kim, Woo Youn},\n  journal = {arXiv preprint arXiv:2310.00681},\n  year = {2023},\n  url = {https://arxiv.org/abs/2310.00681},\n}\n```\n\n\n\n## Future Plan\n\n- Version 2.0.0\n  - Performance Improvement (Provisional: PharmacoNet v2)\n  - SMILES Input (Conformer-free inference)\n- Verison 2.1.0:\n  - Binding Site Detection for Apo Protein Structures\n  - Pharmacophore Customizing\n- Version 3\n  - Binding Pose Prediction\n\n\n\n## Reference\n\n- [PyTorch](https://pytorch.org)\n- [NumPy](https://numpy.org)\n- [Biopython](http://biopython.org)\n- [Open Babel](http://openbabel.org)\n- [Open-Source PyMOL](http://pymol.org) ([github](https://github.com/schrodinger/pymol-open-source))\n- [PyQt5](https://www.riverbankcomputing.com/software/pyqt/)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fseonghwanseo%2Fopenpharmaco","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fseonghwanseo%2Fopenpharmaco","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fseonghwanseo%2Fopenpharmaco/lists"}