{"id":15662334,"url":"https://github.com/rasbt/siteinterlock","last_synced_at":"2025-05-05T23:24:50.807Z","repository":{"id":66172077,"uuid":"65954810","full_name":"rasbt/siteinterlock","owner":"rasbt","description":"A novel approach to pose selection in protein-ligand docking based on graph theory.","archived":false,"fork":false,"pushed_at":"2016-11-22T18:20:17.000Z","size":15987,"stargazers_count":19,"open_issues_count":0,"forks_count":8,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-03-31T00:41:17.494Z","etag":null,"topics":["protein-ligand-docking","protein-structure","python"],"latest_commit_sha":null,"homepage":"http://psa-lab.github.io/siteinterlock/index.html","language":"Python","has_issues":false,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/rasbt.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2016-08-18T01:32:07.000Z","updated_at":"2023-09-08T17:13:48.000Z","dependencies_parsed_at":null,"dependency_job_id":"95d9b53e-5dd0-4a85-9675-66dc2ccb6527","html_url":"https://github.com/rasbt/siteinterlock","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rasbt%2Fsiteinterlock","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rasbt%2Fsiteinterlock/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rasbt%2Fsiteinterlock/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rasbt%2Fsiteinterlock/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/rasbt","download_url":"https://codeload.github.com/rasbt/siteinterlock/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252591559,"owners_count":21773133,"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":["protein-ligand-docking","protein-structure","python"],"created_at":"2024-10-03T13:31:52.503Z","updated_at":"2025-05-05T23:24:50.790Z","avatar_url":"https://github.com/rasbt.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# SiteInterlock\n\n\u003cdiv style=\"max-width:50%;\"\u003e\n\u003cimg src=\"docs/sources/images/logo_small.png\" alt=\"SiteInterlock Logo\"\u003e\n\u003c/div\u003e\n\n---\n\n**NOTE**\n\n**For issues and pull requests, please use https://github.com/psa-lab/siteinterlock**\n\n---\n\n\n***A novel approach to pose selection in protein-ligand docking based on graph theory.***\n\n`siteinterlock` is a Python package for selecting near-native protein-ligand\ndocking poses based upon the hypothesis that interfacial rigidification\nof the protein-ligand interface is an important characteristic that can detect\nthe native ligand binding mode.\n\nThe `siteinterlock` package was developed by Sebastian Raschka in the\n[Protein Structural Analysis \u0026 Design Laboratory](http://www.kuhnlab.bmb.msu.edu)\nat Michigan State University. For additional information on the theory\nbehind the SiteInterlock project, please refer to the accompanying research publication:\n\n- Raschka, Sebastian, Joseph Bemister‐Buffington, and Leslie A. Kuhn. [\"Detecting the native ligand orientation by interfacial rigidity: SiteInterlock.\"](http://onlinelibrary.wiley.com/doi/10.1002/prot.25172/full) *Proteins: Structure, Function, and Bioinformatics* 84.12 (2016): 1888-1901.\n\n\n\n\n# Installation\n\nThe `siteinterlock` package is compatible with Python 2.7.x and Python 3.2 or newer;\nwe recommend using Python 3.5.\nThe package itself does not require external dependencies or libraries.\nIf you don't already have Python installed on your system, you can find more information on how to obtain\nand install Python at [https://www.python.org/downloads/](https://www.python.org/downloads/).\n\nTo produce the input files that are required for the SiteInterlock analysis,\nyou will need to have MSU ProFlex installed.\nMSU ProFlex (formerly called FIRST) predicts the rigid and flexible regions in a protein structure,\ngiven a Protein Data Bank (PDB) file, which you can process according\nto ProFlex instructions to add the necessary\npolar hydrogen atom coordinates. You can find more information\nabout obtaining and installing ProFlex at\n[http://kuhnlab.bmb.msu.edu/software/proflex/index.html](http://kuhnlab.bmb.msu.edu/software/proflex/index.html).\n\n\n## Installing siteinterlock from source\n\n*Please make sure that you are using Python 2.7.x or Python 3.2 or newer\nwhen you are installing and using `siteinterlock`.\nYou can check the version tag of your Python installation\nby executing `python --version` or `python3 --version`\nfrom the command line terminal.*\n\nYou can obtain the latest, stable release of `siteinterlock` from GitHub at [https://github.com/psa-lab/siteinterlock/releases](https://github.com/psa-lab/siteinterlock/releases)\n\n\n1. After clicking on the `Source code (zip)` or `Source code (tar.gz)` download links,\nplease navigate to your download folder and unpack the source code\narchive using your preferred archive-tool.  \n\n2. Next, go into the unzipped `siteinterlock-master` directory,\nand install the `siteinterlock`\npackage by executing `python setup.py install` (the top level directory in the `siteinterlock-master` folder).\n\n3. You may verify your installation by opening a new\nterminal and executing the following command:\n`python -c 'import siteinterlock; print(siteinterlock.__version__)'`, which should print `1.0.0`. If you receive an\n\n4. Now, you will be able to use the SiteInterlock scripts provided\nin the `scripts/` subdirectory from any location on your local drive.\n\n# Documentation\n\nYou can find a detailed user guide in the package documentation that\nis hosted at\n[http://psa-lab.github.io/siteinterlock/index.html](http://psa-lab.github.io/siteinterlock/index.html).\n\nAlternatively, you can view the documentation offline after\ndownloading `siteinterlock` and opening the `index.html` file that is\nlocated in the `docs/html/` subdirectory in your preferred web browser.\n\n---\n\n---\n\nCopyright (C) 2016 Michigan State University  \nDeveloped in the [Protein Structural Analysis \u0026 Design Laboratory](http://www.kuhnlab.bmb.msu.edu)  \nContact Email: kuhnlab@msu.edu\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frasbt%2Fsiteinterlock","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frasbt%2Fsiteinterlock","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frasbt%2Fsiteinterlock/lists"}