{"id":15687599,"url":"https://github.com/rasbt/protein-recognition-index","last_synced_at":"2025-05-07T20:02:12.260Z","repository":{"id":66172062,"uuid":"116623938","full_name":"rasbt/protein-recognition-index","owner":"rasbt","description":"Protein Recognition Index (PRI), measuring the similarity between H-bonding features in a given complex (predicted or designed) and the characteristic H-bond trends from crystallographic complexes","archived":false,"fork":false,"pushed_at":"2018-02-06T07:37:23.000Z","size":593,"stargazers_count":8,"open_issues_count":0,"forks_count":5,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-31T13:35:32.993Z","etag":null,"topics":["bioinformatics","computational-biology","protein-ligand-docking","protein-ligand-interactions","scoring-algorithm"],"latest_commit_sha":null,"homepage":"http://psa-lab.github.io/protein-recognition-index","language":"Python","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/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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-01-08T03:21:26.000Z","updated_at":"2023-09-08T17:34:53.000Z","dependencies_parsed_at":null,"dependency_job_id":"b7336cf0-fc3b-4e83-8c92-10b6a049ba7a","html_url":"https://github.com/rasbt/protein-recognition-index","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%2Fprotein-recognition-index","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rasbt%2Fprotein-recognition-index/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rasbt%2Fprotein-recognition-index/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rasbt%2Fprotein-recognition-index/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/rasbt","download_url":"https://codeload.github.com/rasbt/protein-recognition-index/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252949271,"owners_count":21830151,"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","computational-biology","protein-ligand-docking","protein-ligand-interactions","scoring-algorithm"],"created_at":"2024-10-03T17:50:17.645Z","updated_at":"2025-05-07T20:02:12.209Z","avatar_url":"https://github.com/rasbt.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Protein Recognition Index (PRI)\n\n![](docs/sources/images/pri-logo.png)\n\nThe Protein Recognition Index (PRI) measures the similarity between H-bonding features in a given complex (predicted or designed) and the characteristic H-bond trends from crystallographic complexes based on hydrogen-bond interactions idendified by [Hbind](https://github.com/psa-lab/Hbind) (software for rigorously defining intermolecular H-bonds by donor/acceptor chemistry and geometric constraints).\n\nThe PRI was developed, used, and described in detail in \n\n- Raschka, Sebastian, Alex Wolf, Joseph Bemister‐Buffington, and Leslie A. Kuhn (2018) “Protein-ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes” Journal of Computer-Aided Molecular Design. *Journal of Computer-Aided Molecular Design* (accepted manuscript) [[biorxiv preprint](https://www.biorxiv.org/content/early/2018/02/05/260612)]\n\nDocumentation: https://psa-lab.github.io/protein-recognition-index\n\n\n\u003cbr\u003e\n\u003cbr\u003e\n\u003cbr\u003e\n\n---\n\n## Installation\n\nNo installation is required to execute the Protein Recognition Index software, which is available from the `code` subdirectory in this repository: [`./code/pri-score.py`](./code/pri-score.py). However, a current version of Python is required; we recommend [Python 3.6](https://www.python.org/downloads/release/python-360/) or greater.\n\nIn addition, running `pri-score.py` requires hydrogen-bond interaction tables as generated by [Hbind](http://psa-lab.github.io/Hbind). Hbind is freely available, and for more information on how to install and use it, please visit [http://psa-lab.github.io/Hbind](http://psa-lab.github.io/Hbind).\n\n## Usage\n\nThe Protein Recognition Score software can be executed from the command line and takes an [Hbind](http://psa-lab.github.io/Hbind) interaction table as input, which lists the hydrogen-bond interactions between a protein and its ligand.\n\nThe following example illustrates how to compute the PRI score for the 1KPF [1KPF](https://www.rcsb.org/pdb/explore.do?structureId=1kpf) complex (PKCI-substrate analog) with its ligand `1KPF_AMP.mol2` (adenosine monophsophate). The structures are provided in the \"[example_files/](./example_files)\" subdirectory along with the generated Hbind interaction table.\n\n---\n\n![](docs/sources/images/1kpf_interact.png)\n\n[Interactions between an PKCI-substrate analog ([1KPF](https://www.rcsb.org/pdb/explore.do?structureId=1kpf))  with its ligand (adenosine monophsophate) via [HbindViz](https://github.com/rasbt/HbindViz) and [PyMOL](https://pymol.org); hydrogen atoms not shown]\n\n---\n\nTo compute the PRI score, simply invoke the following command in your terminal:\n\n    python code/pri-score.py example_files/hbind_output.txt\n\nThe resulting output is shown below:\n\n```\nProtein Recognition Index, version 1.0.0\n\nDocumentation: http://psa-lab.github.io/protein-recognition-index\nRaschka, Wolf, Bemister-Buffington, Kuhn (2018)\nProtein Structure and Analysis Lab, MSU (http://kuhnlab.bmb.msu.edu)\n    \nProtein PRI: 252\nLigand PRI: 1584\nPRI: 0.039\n```\n\nThe Protein PRI (PRI-prot) and Ligand PRI (PRI-lig) scores are computed based on the hydrogen bond statistics across 136 non-homologous protein-ligand complexes as described in\n\n- Raschka, Sebastian, Alex Wolf, Joseph Bemister‐Buffington, and Leslie A. Kuhn (2018) “Protein-ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes” Journal of Computer-Aided Molecular Design. *Journal of Computer-Aided Molecular Design* (accepted manuscript) [[biorxiv preprint](https://www.biorxiv.org/content/early/2018/02/05/260612)]\n\nThe PRI is then computed by standardizing the Protein and Ligand PRI scores and adding these, respectively:\n\n![](docs/sources/images/pri-eq.png)\n\nHere, \u0026mu; (mean) and \u0026sigma; (standard deviation) were derived from the 136 PRI-lig and PRI-prot scores computed from the 136 non-homologous complexes.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frasbt%2Fprotein-recognition-index","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frasbt%2Fprotein-recognition-index","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frasbt%2Fprotein-recognition-index/lists"}