{"id":18527227,"url":"https://github.com/jbarnoud/simulation_yellow_pages","last_synced_at":"2026-01-28T20:40:41.078Z","repository":{"id":145284586,"uuid":"159255031","full_name":"jbarnoud/simulation_yellow_pages","owner":"jbarnoud","description":"Inventory of places that host or inventory molecular simulations.","archived":false,"fork":false,"pushed_at":"2018-11-27T01:11:06.000Z","size":2,"stargazers_count":1,"open_issues_count":1,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-10-11T04:04:02.883Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/jbarnoud.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":"2018-11-27T01:08:36.000Z","updated_at":"2023-03-03T15:57:46.000Z","dependencies_parsed_at":null,"dependency_job_id":"843524bc-248f-44c5-ab9a-72d769e6fcaf","html_url":"https://github.com/jbarnoud/simulation_yellow_pages","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/jbarnoud/simulation_yellow_pages","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jbarnoud%2Fsimulation_yellow_pages","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jbarnoud%2Fsimulation_yellow_pages/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jbarnoud%2Fsimulation_yellow_pages/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jbarnoud%2Fsimulation_yellow_pages/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jbarnoud","download_url":"https://codeload.github.com/jbarnoud/simulation_yellow_pages/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jbarnoud%2Fsimulation_yellow_pages/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28851105,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-28T15:15:36.453Z","status":"ssl_error","status_checked_at":"2026-01-28T15:15:13.020Z","response_time":57,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":"2024-11-06T17:54:34.088Z","updated_at":"2026-01-28T20:40:41.060Z","avatar_url":"https://github.com/jbarnoud.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"Yellow pages of molecular simulation sources\n============================================\n\nThis is an attenmpt to inventory places that makes molecular simulations available. This list started in the context of the workshop on [\"Sharing Data from Molecular Simulations\"](https://bioexcel.eu/events/workshop-on-sharing-data-from-molecular-simulations/).\n\nYou can contribute to this list by posting a pull request or an issue.\n\nCollaborative hosting databases\n-------------------------------\n\nDatabases that host simulations and accept external submissions.\n\n### GPCRmd \u003chttp://www.gpcrmd.org\u003e\n\nThis database is at the prototype stage. It allows to search, vizualize and download molecular dynamic simulations of GPCRs. It provides search criteria and analyses specialized for the field.\n\nAggregation databases\n---------------------\n\nDatabases that aggregate simulations hosted somewhere else.\n\n### NMRLipids \u003chttp://www.nmrlipids.fi\u003e\n\nDatabase of simulations for the [NMRLipids project](http://nmrlipids.blogspot.fi). It aggregates and annotates simulations of lipid bilayers carried out with various force field and various conditions. The simulations are mostly hosted on Zenodo.\n\n### MDAnalysisData \u003chttps://www.mdanalysis.org/MDAnalysisData/index.html\u003e\n\nCollection of links to dataset used to demonstrate, teach, or test MDAnalysis. The collection can be accessed *via* the website, or throught a python library.\n\nSingle-lab databases\n--------------------\n\nDatabases that host simulations but do not accept external submissions.\n\n### MemProtMD \u003chttp://memprotmd.bioch.ox.ac.uk\u003e\n\nCollection of coarse grained molecular dynamics simulations of membrane proteins in a membrane environment carried out with an automatic pipeline. The database allows to search proteins, to vizualize snapshots of the simulations, to see and download the result of analyses relevant for membrane proteins, and to download starting files to carry out a simulation of the system.\n\n### MoDEL \u003chttp://mmb.pcb.ub.es/MoDEL/\u003e\n\nOther places\n------------\n\n* [Datasets on Zenodo that includes a TPR](https://zenodo.org/search?page=1\u0026size=20\u0026q=filetype:tpr#)\n* [Datasets on Zenodo that include a DCD file](https://zenodo.org/search?page=1\u0026size=20\u0026q=filetype:dcd)\n* [\"molecular dynamics\" in Google Dataset Search](\u003chttps://toolbox.google.com/datasetsearch/search?query=molecular dynamics\u003e)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjbarnoud%2Fsimulation_yellow_pages","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjbarnoud%2Fsimulation_yellow_pages","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjbarnoud%2Fsimulation_yellow_pages/lists"}