{"id":23280268,"url":"https://github.com/moldyn/hp35-desres","last_synced_at":"2026-01-19T06:02:17.592Z","repository":{"id":111463429,"uuid":"222400471","full_name":"moldyn/HP35-DESRES","owner":"moldyn","description":"DESRES trajectory of wild type HP-35 at 360K","archived":false,"fork":false,"pushed_at":"2023-05-16T08:45:43.000Z","size":38,"stargazers_count":5,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-09-05T13:39:34.601Z","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":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/moldyn.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":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2019-11-18T08:36:27.000Z","updated_at":"2025-01-29T08:40:22.000Z","dependencies_parsed_at":null,"dependency_job_id":"a4f47525-ec2e-47bf-b950-bddceaf31ad4","html_url":"https://github.com/moldyn/HP35-DESRES","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/moldyn/HP35-DESRES","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moldyn%2FHP35-DESRES","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moldyn%2FHP35-DESRES/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moldyn%2FHP35-DESRES/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moldyn%2FHP35-DESRES/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/moldyn","download_url":"https://codeload.github.com/moldyn/HP35-DESRES/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moldyn%2FHP35-DESRES/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28562238,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-19T03:31:16.861Z","status":"ssl_error","status_checked_at":"2026-01-19T03:31:15.069Z","response_time":67,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: 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":"2024-12-19T23:31:23.912Z","updated_at":"2026-01-19T06:02:17.578Z","avatar_url":"https://github.com/moldyn.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# HP35-DESRES\n\n## Citations\nUsing any file from this repository, please cite the following article:\n\u003e S. Piana, K. Lindorff-Larsen, and D. E. Shaw,  \n\u003e *Protein folding kinetics and thermodynamics from atomistic simulation*,  \n\u003e Proc. Natl. Acad. Sci. USA 109, 17845 (2012)  \n\u003e doi: [10.1073/pnas.1201811109](https://doi.org/10.1073/pnas.1201811109)\n\n## Provided Data\nThe time series of three different internal coordinate representations of the\nNle/Nle mutant of the villin headpiece (HP35), generated from a 300μs long\nmolecular dynamics simulation (Amber99SB-ILDN) at 360K, are given. Please read\nthe license carefully before use.\n\u003e **DEPENDENCY**: [git-lfs](https://git-lfs.github.com) is needed for large file support\n\n1. `hp35.dihs`: backbone dihedral angels given [degrees]\n1. `hp35.dihs.shifted`: maximum-gap shifted backbone dihedral angels [rad]\n1. `hp35.crystaldists`: the atom distances of all contacts occurring in the crystal structure 2f4k [nm]\n1. `hp35.mindists`: all minimal distances occurring more frequently than 30% [nm]\n1. `hp35.mindists2`: improved distances definition with all atom pairwise distances occurring more frequently than 30% [nm]\n\n### Backbone Dihedral Angles\nThe time series of all backbone dihedral angles from residue 2 to residue 34\nare given in the file `hp35.dihs` (in degrees !), while in `hp35.dihs.shifted`\nthe maximal gap shifting method\n([Sittel et al. 2017](https://doi.org/10.1063/1.4998259)) was applied to allow\nnon-periodic treatment of the angles.\n\nThe columns correspond to\n\n$$ \\phi_2~\\psi_2~\\phi_3~\\psi_3~\\ldots~\\phi_{33} ~\\psi_{33} ~\\phi_{34} ~\\psi_{34} $$\n\nwhich can be also found in the file `hp35.dihs.names`.\n\n### Contact Distances\nThe time series of all minimal distances $d_{ij}$ using the following two\ndifferent approaches suggested by [Nagel et al.\n2023](https://doi.org/10.48550/ARXIV.2303.03814). For `hp35.mindists` the\ndistance between the residues $i$ and $j$ is given by the minimal distance of\nthe heavy atoms $n\\in i$, $m\\in j$, so\n\n$$ d_{ij}(t) = \\min_{n,m} |\\mathbf{r}_ {i, n}(t) - \\mathbf{r}_ {i, n}(t)| $$\n\nand a contact distance must be below $0.45\\:\\text{nm}$\nwith probability $P_{ij}\\ge 0.3$.\n\nThe second definition, used in `hp35.mindists2`, takes the minimum only over\nall atomic distances $n$, $m$ which are formed more frequent than $0.3$, so\n\n$$ d_{ij}(t) = \\min_{P_{n,m}\\ge 0.3} |\\mathbf{r}_ {i, n}(t) - \\mathbf{r}_ {i,n}(t)|\\;.$$\n\nThe indices corresponding to each column can be found in `hp35.mindists.ndx`\nand `hp35.mindists2.ndx`, respectively.\n\nUsing these contact definitions, please cite:\n\u003e D. Nagel, S. Sartore, and G. Stock,  \n\u003e *Selecting Features for Markov Modeling: A Case Study on HP35*,  \n\u003e J. Chem. Theory Comput., submitted  \n\u003e doi: [10.48550/ARXIV.2303.03814](https://doi.org/10.48550/ARXIV.2303.03814)\n\n### Getting-Started\nQuick-start to check and unzip all datasets: \n``` \ngit clone https://github.com/moldyn/HP35-DESRES.git\ncd HP35-DESRES\n# check if corrupt\nfor data in hp35.*.bz2; do\n  bunzip2 -t $data \u0026\u003e/dev/null || echo \"file $data corrupt, please download again.\"\ndone\n# unzip all\nfor data in hp35.*.bz2; do\n  bunzip2 -k $data\ndone\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmoldyn%2Fhp35-desres","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmoldyn%2Fhp35-desres","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmoldyn%2Fhp35-desres/lists"}