{"id":17255236,"url":"https://github.com/unixjunkie/binana","last_synced_at":"2025-03-26T08:16:09.378Z","repository":{"id":144782257,"uuid":"464713157","full_name":"UnixJunkie/BINANA","owner":"UnixJunkie","description":"mirror of https://git.durrantlab.pitt.edu/jdurrant/binana/","archived":false,"fork":false,"pushed_at":"2022-03-01T02:15:54.000Z","size":6169,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-01-31T09:31:33.642Z","etag":null,"topics":["docking","post-processing","protein-ligand"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/UnixJunkie.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGES.md","contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE.md","code_of_conduct":"CODE_OF_CONDUCT.md","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":"2022-03-01T02:15:35.000Z","updated_at":"2023-07-04T07:14:26.000Z","dependencies_parsed_at":null,"dependency_job_id":"7daddbff-4b9b-4654-946e-eccce20b1ff4","html_url":"https://github.com/UnixJunkie/BINANA","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FBINANA","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FBINANA/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FBINANA/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FBINANA/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/UnixJunkie","download_url":"https://codeload.github.com/UnixJunkie/BINANA/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245615010,"owners_count":20644376,"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":["docking","post-processing","protein-ligand"],"created_at":"2024-10-15T07:11:01.984Z","updated_at":"2025-03-26T08:16:09.355Z","avatar_url":"https://github.com/UnixJunkie.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Introduction\n\nBINANA (BINding ANAlyzer) is a python-implemented algorithm for analyzing ligand\nbinding. The program identifies key binding characteristics like hydrogen bonds,\nsalt bridges, and pi interactions. As input, BINANA accepts receptor and ligand\nfiles in the PDBQT (preferred) or PDB formats. PDBQT files can be generated from\nthe more common PDB file format using the [free converter provided with\nAutoDockTools](http://mgltools.scripps.edu/downloads). As output, BINANA\nidentifies and describes key protein/ligand interactions.\n\n# Citation\n\nIf you use BINANA in your work, please cite:\n\nBINANA: A Novel Algorithm for Ligand-Binding Characterization. Durrant JD,\nMcCammon JA. J Mol Graph Model. 2011 Apr; 29(6): 888-893. doi:\n10.1016/j.jmgm.2011.01.004\n\n# License\n\nBINANA 2.1 is released under the [Apache License, Version\n2.0](https://opensource.org/licenses/Apache-2.0). \n\n# Description of select directories and files\n\nThe BINANA Git repository is hosted at\n[http://git.durrantlab.com/jdurrant/binana](http://git.durrantlab.com/jdurrant/binana).\n\n| Directory/File                    | Description\n|-----------------------------------|------------------------------------------\n| `./python/`                       | All Python code\n| `./python/run_binana.py`          | Script for command-line use\n| `./python/binana/`                | Python library (e.g., `import binana`)\n| `./python/example/Examples.ipynb` | Jupyter notebook, Python-library demo\n| `./javascript/lib/`               | JavaScript library\n| `./javascript/lib/Examples.ipynb` | Jupyter notebook, JavaScript-library demo\n| `./javascript/lib/examples.html`  | HTML file, JavaScript-library demo\n| `./web_app/`                      | Web app\n| `./web_app/src/`                  | Web-app source code\n| `./INTERACTIONS.md`               | Descriptions of the detected interactions.\n\n# Locations of BINANA tutorials\n\n## Command-line use\n\nSee `./python/COMMAND_LINE_USE.md` in the Git repository for detailed instructions.\nHere is a simple example:\n\n```bash\ncd python\npython3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt -output_dir /path/to/output/directory/\n```\n\n## Python library\n\nThe following files in the Git repository describe how to use BINANA as a Python\nlibrary that can be accessed from other Python scripts:\n\n- `./python/example/Examples.ipynb`: A Jupyter notebook demonstrating use.\n- `./python/example/Examples.ipynb.pdf`: A PDF version of the notebook, for\n  those who don't use Jupyter.\n- `./python/example/Examples.md`: A Markdown version of the notebook.\n\n## JavaScript library\n\nThese files describe how to use BINANA as a JavaScript library that can be\naccessed from the web browser (e.g., from web apps).\n\n- `./javascript/lib/Examples.ipynb`: A Jupyter notebook demonstrating use.\n- `./javascript/lib/Examples.ipynb.pdf`: A PDF version of the notebook, for\n  those who don't use Jupyter.\n- `./javascript/lib/examples.html`: An HTML file demonstrating use.\n\n## Web-browser app\n\nA [video tutorial](https://youtu.be/BMnSYvH4Qwg) describes how to use the\n[BINANA web-browser app](http://durrantlab.com/binana).","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Fbinana","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Funixjunkie%2Fbinana","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Fbinana/lists"}