{"id":15347387,"url":"https://github.com/vtlim/hv1","last_synced_at":"2026-03-19T17:54:47.253Z","repository":{"id":182914674,"uuid":"70876947","full_name":"vtlim/Hv1","owner":"vtlim","description":"Free energy perturbation calculations for Hv1 protein","archived":false,"fork":false,"pushed_at":"2020-01-23T01:07:02.000Z","size":7722,"stargazers_count":0,"open_issues_count":1,"forks_count":1,"subscribers_count":0,"default_branch":"master","last_synced_at":"2025-07-13T11:49:02.134Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://www.nature.com/articles/s41598-020-70369-4","language":"Tcl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/vtlim.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}},"created_at":"2016-10-14T05:28:40.000Z","updated_at":"2024-02-02T21:20:41.000Z","dependencies_parsed_at":"2023-07-22T04:10:02.274Z","dependency_job_id":null,"html_url":"https://github.com/vtlim/Hv1","commit_stats":null,"previous_names":["vtlim/hv1"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/vtlim/Hv1","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vtlim%2FHv1","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vtlim%2FHv1/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vtlim%2FHv1/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vtlim%2FHv1/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/vtlim","download_url":"https://codeload.github.com/vtlim/Hv1/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vtlim%2FHv1/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29167870,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-06T15:38:29.831Z","status":"ssl_error","status_checked_at":"2026-02-06T15:37:48.592Z","response_time":59,"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":"2024-10-01T11:33:06.979Z","updated_at":"2026-02-06T16:03:21.170Z","avatar_url":"https://github.com/vtlim.png","language":"Tcl","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n# Hv1\n\nThis repository was created to house scripts related to molecular dynamics simulations on the Hv1 protein. \nThe subdirectories were numbered to maintain file organization across multiple clusters but not all subdirectories have scripts here. \nOther components were complex enough to warrant their own repositories, which are hyperlinked. \nThe most relevant and up-to-date preparation and analysis scripts in this repo are those for FEP calculations.\n\n1. **Docking**\n2. **Pose analysis**\n3. **Ligand in water box** - no scripts\n4. **FEP**\n5. **QM dihedral scan** - see this [repo](https://github.com/vtlim/dihedral-scan)\n6. **QM tautomers** - no scripts\n7. **MM dihedral scan** - umbrella sampling, for `extraBonds` restraints see #5.\n8. **Permeation** - see this [repo](https://github.com/vtlim/permeability)\n9. **REST2**\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvtlim%2Fhv1","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvtlim%2Fhv1","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvtlim%2Fhv1/lists"}