{"id":15359625,"url":"https://github.com/jhsmit/hdxrate","last_synced_at":"2025-04-15T07:23:08.497Z","repository":{"id":60722439,"uuid":"309354423","full_name":"Jhsmit/HDXrate","owner":"Jhsmit","description":"Calculate protein amide hydrogen exchange rate","archived":false,"fork":false,"pushed_at":"2024-07-25T15:13:43.000Z","size":362,"stargazers_count":5,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-04-09T01:52:11.666Z","etag":null,"topics":["hdx-ms"],"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/Jhsmit.png","metadata":{"files":{"readme":"README.rst","changelog":"HISTORY.rst","contributing":"CONTRIBUTING.rst","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":"AUTHORS.rst","dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-11-02T11:48:52.000Z","updated_at":"2025-02-24T03:33:38.000Z","dependencies_parsed_at":"2022-10-03T21:01:22.362Z","dependency_job_id":"fa91fd73-9e92-4f93-8a6c-d7812102262f","html_url":"https://github.com/Jhsmit/HDXrate","commit_stats":{"total_commits":72,"total_committers":2,"mean_commits":36.0,"dds":0.01388888888888884,"last_synced_commit":"90405c76a86346288f6d99aea123835e09fc4ab0"},"previous_names":[],"tags_count":6,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Jhsmit%2FHDXrate","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Jhsmit%2FHDXrate/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Jhsmit%2FHDXrate/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Jhsmit%2FHDXrate/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Jhsmit","download_url":"https://codeload.github.com/Jhsmit/HDXrate/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":249024395,"owners_count":21200111,"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":["hdx-ms"],"created_at":"2024-10-01T12:45:26.430Z","updated_at":"2025-04-15T07:23:08.477Z","avatar_url":"https://github.com/Jhsmit.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"=======\nHDXrate\n=======\n\n\n.. image:: https://img.shields.io/pypi/v/hdxrate.svg\n        :target: https://pypi.python.org/pypi/hdxrate\n\n.. image:: https://readthedocs.org/projects/hdxrate/badge/?version=latest\n        :target: https://hdxrate.readthedocs.io/en/latest/?badge=latest\n        :alt: Documentation Status\n\n.. image:: https://zenodo.org/badge/309354423.svg\n   :target: https://zenodo.org/badge/latestdoi/309354423\n\n\nPython package for HDX intrinsic exchange rate calculation. \n\n.. raw:: html\n\n    \u003cimg src=\"HDX_rate.jpg\" width=\"400\" height=\"400\" alt=\"DALL-E generated image\" align=\"center\"\u003e\n\nThe calculations are based on the following papers:\n\n  Bai, Y., Milne, J. S., Mayne, L. \u0026 Englander, S. W. Primary structure effects on peptide group hydrogen exchange. `Proteins Structure, Function, and Bioinformatics \u003chttps://doi.org/10.1002/prot.340170110\u003e`__ 17, 75–86 (1993)\n\n  Connelly, G. P., Bai, Y., Jeng, M.-F. \u0026 Englander, S. W. Isotope effects in peptide group hydrogen exchange. `Proteins \u003chttp://doi.wiley.com/10.1002/prot.340170111\u003e`__ 17, 87–92 (1993).\n\n\n  Mori, S., Zijl, P. C. M. van \u0026 Shortle, D. Measurement of water–amide proton exchange rates in the denatured state of staphylococcal nuclease by a magnetization transfer technique. `Proteins Structure, Function, and Bioinformatics \u003chttps://doi.org/10.1002/(SICI)1097-0134(199707)28:3%3C325::AID-PROT3%3E3.0.CO;2-B\u003e`__ 28, 325–332 (1997)\n  \n  Nguyen, D., Mayne, L., Phillips, M. C. \u0026 Walter Englander, S. Reference Parameters for Protein Hydrogen Exchange Rates. `J. Am. Soc. Mass Spectrom.  \u003chttps://doi.org/10.1007/s13361-018-2021-z\u003e`__ 29, 1936–1939 (2018).\n\n..\n   1.Rubinson, K. A. Practical corrections for p(H,D) measurements in mixed H 2 O/D 2 O biological buffers. Anal. Methods 9, 2744–2750 (2017).\n\n\nSee also the excel sheet on the Englander group website: http://hx2.med.upenn.edu/download.html\n\n\n* Free software: GNU General Public License v3\n\n\nFeatures\n--------\n\nCalculate intrinsic rate of amide hydrogen exchange in proteins.\n\nInstallation\n------------\n\n::\n\n   $ pip install hdxrate\n\nor\n\n::\n\n   $ conda install -c conda-forge hdxrate\n\nUsage\n-----\n\n::\n\n   \u003e\u003e\u003e from hdxrate import k_int_from_sequence\n   \u003e\u003e\u003e k_int_from_sequence('HHHHH', 300, 7.)\n   array([0.00000000e+00, 2.62430718e+03, 6.29527446e+01, 6.29527446e+01,\n       9.97734191e-01])\n\n\nCredits\n-------\n\nHDXrate implementation is based on PSX intrinsic rate calculation\nhttps://github.com/Niels-Bohr-Institute-XNS-StructBiophys/PSX\n\n Pedersen, M. C. et al. PSX, Protein–Solvent Exchange: software for calculation of deuterium-exchange effects in small-angle neutron scattering measurements from protein coordinates. `J Appl Cryst \u003chttps://doi.org/10.1107/S1600576719012469/\u003e`__ 52, 1427–1436 (2019).\n\n\n\nMaintenance\n```````````\n\n* Jochem Smit \u003cjhsmit@gmail.com\u003e / \u003cjochem.smit@kuleuven.be\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjhsmit%2Fhdxrate","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjhsmit%2Fhdxrate","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjhsmit%2Fhdxrate/lists"}