{"id":16694452,"url":"https://github.com/ricalessandri/martini3-small-molecules","last_synced_at":"2025-05-08T23:42:01.854Z","repository":{"id":37299344,"uuid":"387129352","full_name":"ricalessandri/Martini3-small-molecules","owner":"ricalessandri","description":"Martini 3 small-molecule database","archived":false,"fork":false,"pushed_at":"2024-08-21T20:54:24.000Z","size":29216,"stargazers_count":56,"open_issues_count":18,"forks_count":11,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-01-26T04:06:42.840Z","etag":null,"topics":["coarse-graining","database","martini3","molecular-dynamics","small-molecules"],"latest_commit_sha":null,"homepage":"https://doi.org/10.1002/adts.202100391","language":"Shell","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/ricalessandri.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":"2021-07-18T08:41:05.000Z","updated_at":"2025-01-02T07:00:01.000Z","dependencies_parsed_at":"2023-01-19T11:30:48.423Z","dependency_job_id":"66f7417b-0dca-4dc5-8f97-53afa4a517e2","html_url":"https://github.com/ricalessandri/Martini3-small-molecules","commit_stats":{"total_commits":43,"total_committers":1,"mean_commits":43.0,"dds":0.0,"last_synced_commit":"df4e2621a81d5470fd3be827b7ff52719b25b1cd"},"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ricalessandri%2FMartini3-small-molecules","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ricalessandri%2FMartini3-small-molecules/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ricalessandri%2FMartini3-small-molecules/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ricalessandri%2FMartini3-small-molecules/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ricalessandri","download_url":"https://codeload.github.com/ricalessandri/Martini3-small-molecules/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":238048493,"owners_count":19407877,"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":["coarse-graining","database","martini3","molecular-dynamics","small-molecules"],"created_at":"2024-10-12T16:45:59.051Z","updated_at":"2025-02-10T03:01:43.501Z","avatar_url":"https://github.com/ricalessandri.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n# Martini 3 small-molecule database\n\nThis GitHub repository contains a collection of Martini 3 models for small molecules.\n\nIf you use or wish to cite the Martini 3 small-molecule database, please refer to the following publication:\n\n- R. Alessandri, J. Barnoud, A.S. Gertsen, I. Patmanidis, A.H. de Vries, P.C.T. Souza, S.J. Marrink.\n  \"Martini 3 Coarse-Grained Force Field: Small Molecules\", *Adv. Theory Simul.* **2022**, *5*, 2100391 [(open-access)](https://doi.org/10.1002/adts.202100391).\n \nAdditional references should be cited for particular models. Please check the header of the model for details.\n \n\n\n## Quick links\n\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"./models/martini_v3.0.0_small_molecules_v1.itp\"\u003e\u003cb\u003eCurrent \u003cem\u003eitp collection\u003c/em\u003e of Martini 3 small molecule models\u003c/b\u003e\u003c/a\u003e\n\u003c/p\u003e\n\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"./LIBRARY.md\"\u003e\u003cb\u003eCurrent \u003cem\u003elookup table\u003c/em\u003e of Martini 3 small molecule models\u003c/b\u003e\u003c/a\u003e\n\u003c/p\u003e\n\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"./tutorials/M3tutorials--parameterizing-a-new-small-molecule.md\"\u003e\u003cb\u003eTutorial: Parametrizing a new small molecule with Martini 3\u003c/b\u003e\u003c/a\u003e\n\u003c/p\u003e\n\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"./tutorials/building_block_table.pdf\"\u003e\u003cb\u003eBuilding block reference table to guide bead type choice\u003c/b\u003e\u003c/a\u003e\n\u003c/p\u003e\n\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://d3ebrx6qufncts.cloudfront.net/0_Tutorials/Lectures/videos/2021-09-02_MartiniWorkshop2021_Small_molecules.mp4\"\u003e\u003cb\u003eTalk about Martini 3 small molecules at the Martini Workshop 2021\u003c/b\u003e\u003c/a\u003e\n  (\u003ca href=\"http://cgmartini.nl/images/stories/workshop2021/lectures/second/riccardo/2021-09-02_MartiniWorkshop2021_Small_molecules-vFINAL.pdf\"\u003e\u003cb\u003eslides\u003c/b\u003e\u003c/a\u003e)\n\u003c/p\u003e\n\n\n## Brief summary of repo content\n\nThis repo contains:\n\n- Martini 3 small molecule models (and supporting files, e.g., atomistic-to-Martini mapping files):\n  [models/](./models)\n\n- Tutorials and reference material to build your own Martini 3 model: \n  [tutorials/](./tutorials)\n\n- The procedures used to compute properties: \n  [procedures/](./procedures)\n  \nPlease make sure to check the `README.md` in each subfolder for some more information and details. \n\n\n\n## Contributing\n\nContributions are welcome as [bug reports] and [pull requests] from everyone.\n\n\n\n## License\n\n\u003cpre\u003e\u003ccode\u003e\nCopyright 2021 University of Groningen\n\nLicensed under the Apache License, Version 2.0 (the \"License\");\nyou may not use this file except in compliance with the License.\nYou may obtain a copy of the License at\n\n        http://www.apache.org/licenses/LICENSE-2.0\n\nUnless required by applicable law or agreed to in writing, software\ndistributed under the License is distributed on an \"AS IS\" BASIS,\nWITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\nSee the License for the specific language governing permissions and\nlimitations under the License.\n\u003c/code\u003e\u003c/pre\u003e\n\nThe [full text of the license](https://github.com/ricalessandri/Martini3-small-molecules/blob/master/LICENSE) \nis available in the source repository.\n\n\n\n[bug reports]: https://github.com/ricalessandri/Martini3-small-molecules/issues\n[pull requests]: https://github.com/ricalessandri/Martini3-small-molecules/pulls\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fricalessandri%2Fmartini3-small-molecules","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fricalessandri%2Fmartini3-small-molecules","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fricalessandri%2Fmartini3-small-molecules/lists"}