{"id":19339510,"url":"https://github.com/becksteinlab/pdb_ion_survey","last_synced_at":"2025-09-06T15:43:46.148Z","repository":{"id":137558351,"uuid":"46756179","full_name":"Becksteinlab/PDB_Ion_Survey","owner":"Becksteinlab","description":"A survey of ion coordination geometries in proteins.","archived":false,"fork":false,"pushed_at":"2022-06-17T22:09:42.000Z","size":2876,"stargazers_count":1,"open_issues_count":5,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-01-06T10:48:27.444Z","etag":null,"topics":["protein-structure","proteins","science"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"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/Becksteinlab.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":"2015-11-24T00:14:50.000Z","updated_at":"2022-06-17T22:09:45.000Z","dependencies_parsed_at":null,"dependency_job_id":"b9a712e3-3cee-4a95-b66f-06e328b5ecec","html_url":"https://github.com/Becksteinlab/PDB_Ion_Survey","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/Becksteinlab%2FPDB_Ion_Survey","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2FPDB_Ion_Survey/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2FPDB_Ion_Survey/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2FPDB_Ion_Survey/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Becksteinlab","download_url":"https://codeload.github.com/Becksteinlab/PDB_Ion_Survey/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240442511,"owners_count":19801914,"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-structure","proteins","science"],"created_at":"2024-11-10T03:22:34.629Z","updated_at":"2025-02-24T08:23:15.268Z","avatar_url":"https://github.com/Becksteinlab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Protein Ion Coordination Survey\n\n[![Join the chat at https://gitter.im/Becksteinlab/PDB_Ion_Survey](https://badges.gitter.im/Becksteinlab/PDB_Ion_Survey.svg)](https://gitter.im/Becksteinlab/PDB_Ion_Survey?utm_source=badge\u0026utm_medium=badge\u0026utm_campaign=pr-badge\u0026utm_content=badge)\n\nAs part of the [BioXFEL Ed Scientific Villages at ASU](https://www.bioxfel.org/education/high-school-learning-communities) program, [@kaceyreidy](https://github.com/kaceyreidy) is building a reusable data acquisition and analysis pipeline to characterize the interactions between ions and proteins. \n\nThe input data are crystal structures from the [Protein Databank](http://www.pdb.org). [MDAnalysis](http://www.mdanalysis.org) is used to analyze the data. The initial focus is on a statistical analysis of the coordination numbers of ions, in particular oxygen-cation interactions.\n\n# How to Use\n\n* Use get_proteins to search the PDB for molecules of a certain type with a specified ion.\n* Use get_pdb_file to download pdb files from the PDB.\n* Use en to create radial distributions for oxygen atoms around an ion.\n* Use cume to create a cumulative radial distribution function for oxygen atoms around an ion.\n* Use gee to create a density radial distribution function for oxygen atoms around an ion.\n* Talk to Martin Blech to use unparse or _emit.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecksteinlab%2Fpdb_ion_survey","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbecksteinlab%2Fpdb_ion_survey","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecksteinlab%2Fpdb_ion_survey/lists"}