{"id":24523617,"url":"https://github.com/m4marvin/plb_jnu","last_synced_at":"2026-05-08T09:35:37.616Z","repository":{"id":271986708,"uuid":"915189219","full_name":"M4Marvin/plb_jnu","owner":"M4Marvin","description":"Deep Learning Framework for Protein-Ligand Binding Affinity Prediction  ","archived":false,"fork":false,"pushed_at":"2025-01-28T17:45:58.000Z","size":48045,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-15T14:12:39.009Z","etag":null,"topics":["bioinformatics","biology","chemistry","com","computational-biology","deep-learning","ligand","protein","python","pytorch"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","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/M4Marvin.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":"2025-01-11T07:37:34.000Z","updated_at":"2025-01-28T17:46:02.000Z","dependencies_parsed_at":"2025-01-11T08:29:39.450Z","dependency_job_id":"59d3245b-8c6a-4d04-91ff-3cd1b966ef16","html_url":"https://github.com/M4Marvin/plb_jnu","commit_stats":null,"previous_names":["m4marvin/plb_jnu"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/M4Marvin%2Fplb_jnu","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/M4Marvin%2Fplb_jnu/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/M4Marvin%2Fplb_jnu/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/M4Marvin%2Fplb_jnu/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/M4Marvin","download_url":"https://codeload.github.com/M4Marvin/plb_jnu/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243738979,"owners_count":20340002,"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":["bioinformatics","biology","chemistry","com","computational-biology","deep-learning","ligand","protein","python","pytorch"],"created_at":"2025-01-22T04:16:07.072Z","updated_at":"2026-05-08T09:35:37.573Z","avatar_url":"https://github.com/M4Marvin.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Deep Learning Framework for Protein-Ligand Binding Affinity Prediction\n\n## Overview\n\nThis research project implements a novel deep learning architecture combining 3D Convolutional Neural Networks (CNNs) and Graph Convolutional Networks (GCN) to predict protein-ligand binding affinities. The model processes structural and chemical information through parallel networks before combining outputs for final prediction.\n\n## Architecture\n\n- Dual 3D-CNN branches processing voxelized molecular representations (48×48×48×19)\n- Graph Convolutional Network (GCN) for molecular topology\n- Multi-Layer Perceptron (MLP) for final affinity prediction\n\n## Dataset\n\n- Based on the PDBbind dataset\n- Preprocessed molecular structures with computed charges (MOL2 format)\n- Voxelized representations for CNN input\n\n## Requirements\n\n```python\ntorch\u003e=1.9.0\nnumpy\npandas\nh5py\nbiopandas\n```\n\n## Project Structure\n\n``` bash\n├── LICENSE\n├── README.md\n├── data\n│   ├── pdb_bind\n│   │   ├── refined-set              # Refined Set Data\n│   │   └── v2020-other-PL          # General Set\n│   └── sample_data\n├── notebooks\n└── src\n    ├── models\n    ├── preprocessing\n    └── training\n```\n\n## Setup\n\n- to be added.\n\n## Usage\n\n- to ber added.\n\n\u003c!-- ## Citation\n[Add your paper details once published] --\u003e\n\n## License\n\nMIT\n\n## Contact\n\n[Your Name]\n[Your Institution]\n[Your Email]\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fm4marvin%2Fplb_jnu","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fm4marvin%2Fplb_jnu","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fm4marvin%2Fplb_jnu/lists"}