{"id":17255161,"url":"https://github.com/unixjunkie/pli","last_synced_at":"2025-07-29T21:32:22.928Z","repository":{"id":144782612,"uuid":"91643351","full_name":"UnixJunkie/PLI","owner":"UnixJunkie","description":"mirror of https://bitbucket.org/AstexUK/pli","archived":false,"fork":false,"pushed_at":"2017-05-18T03:24:13.000Z","size":83840,"stargazers_count":1,"open_issues_count":0,"forks_count":37,"subscribers_count":1,"default_branch":"master","last_synced_at":"2024-10-15T07:11:18.654Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"C","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/UnixJunkie.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"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":"2017-05-18T03:11:08.000Z","updated_at":"2022-07-15T18:00:27.000Z","dependencies_parsed_at":null,"dependency_job_id":"1a502edf-96c8-4995-b1fb-81bdb94d8404","html_url":"https://github.com/UnixJunkie/PLI","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FPLI","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FPLI/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FPLI/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FPLI/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/UnixJunkie","download_url":"https://codeload.github.com/UnixJunkie/PLI/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":228048818,"owners_count":17861448,"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":"2024-10-15T07:10:50.447Z","updated_at":"2024-12-04T05:22:36.015Z","avatar_url":"https://github.com/UnixJunkie.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Astex PLI #\n\nPLI is a program developed at Astex Pharmaceuticals for scoring protein-ligand \ninteractions. Interacting atoms are defined using a [modified][mcconkey] \n[Voronoi partitioning][voronoi] and interaction propensities (including geometric \npreferences) have been derived from over 30,000 [PDB][pdb] entries.\n\nMuch of the PLI methodology was published recently:\n\n**Protein-Ligand-Informatics force field (PLIff): towards a fully knowledge driven “force field” for biomolecular interactions**\n\nM.L. Verdonk, R.F. Ludlow, I. Giangreco, and P.C. Rathi\n\n*J. Med. Chem., Just Accepted Manuscript*\n\nDOI: [10.1021/acs.jmedchem.6b00716][doi]\n\nWe are actively developing the PLI code and will release an updated version in July 2016.\n\n## Features ##\n* Score protein-ligand interactions (for example docking/VS poses)\n* Solvent Mapping\n* Generate Interaction Maps for Donor/Acceptor/Lipophile etc.\n* Rich atom-typing \n\n## Installation ##\n\n### System Requirements ###\n\nPLI is written in C and has been developed and tested on 64-bit Linux (CentOS) \nusing the gcc compiler. It has no major external dependencies.\n\n### Obtaining the Code ###\n\n#### Download ####\n* A zip of the current repository and tagged releases (as they become\n  available) can be found at [bitbucket][downloads]. \n\n#### Via Git ####\n* You can fork the repository on bitbucket (you will need an account)\nor clone the repository from the command line\n```bash\ngit clone https://bitbucket.org/AstexUK/pli.git\n```\n\n### Installing ###\n\nOnce you have obtained the code (either by extracting a snapshot or\ncloning the repository:\n\n* `cd` to the directory `\u003cdir\u003e`\n* Type `make` in `\u003cdir\u003e`. This should compile the code and create a binary `\u003cdir\u003e/bin/pli`.\n* Set the environment variable `PLI_DIR` to `\u003cdir\u003e`, e.g. for bash:\n```bash\nPLI_DIR=/path/to/pli\nexport PLI_DIR\n```\n* Try running one of the examples in the examples directory, e.g:\n```bash\ncd $PLI_DIR/examples\n$PLI_DIR/bin/pli -settings $PLI_DIR/examples/1a9u_contacts.pli\n```\n\n## Modes ##\nTo see a list of modes and command-line options run\n```sh\n$PLI_DIR/bin/pli -help\n```\n\n## Get In Touch ##\nIf you have questions about PLI or have found it useful, let us know, on bitbucket or \nby email: \"pli-at-astx-dot-com\"\n\n## Licence ##\nApache 2.0 License, see licence.txt for details. \n\n## Acknowledgements ##\n* Brendan McConkey - for the capped and weighted Voronoi partitioning code (see the [original publication][mcconkey])\n* John Burkardt - whose [SPHERE_LEBEDEV_RULE][lebedev] program was used to calculate lebedev points.\n* The [PDB][pdb] - and the thousands of authors who have deposited X-ray structures of protein-ligand complexes.\n\n[voronoi]: http://mathworld.wolfram.com/VoronoiDiagram.html\n[pdb]: http://www.wwpdb.org/\n[downloads]: https://bitbucket.org/AstexUK/pli/downloads\n[mcconkey]: http://dx.doi.org/10.1093/bioinformatics/18.10.1365\n[lebedev]: https://people.sc.fsu.edu/~jburkardt/c_src/sphere_lebedev_rule/sphere_lebedev_rule.html\n[doi]: http://dx.doi.org/10.1021/acs.jmedchem.6b00716","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Fpli","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Funixjunkie%2Fpli","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Fpli/lists"}