{"id":20915664,"url":"https://github.com/markovmodel/decomposed_msms","last_synced_at":"2026-04-27T14:05:06.423Z","repository":{"id":72544770,"uuid":"240042112","full_name":"markovmodel/decomposed_msms","owner":"markovmodel","description":null,"archived":false,"fork":false,"pushed_at":"2022-02-14T13:30:53.000Z","size":561,"stargazers_count":3,"open_issues_count":0,"forks_count":0,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-12-28T01:51:04.490Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","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/markovmodel.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":"2020-02-12T15:08:27.000Z","updated_at":"2025-05-12T14:20:37.000Z","dependencies_parsed_at":"2023-03-06T22:30:33.338Z","dependency_job_id":null,"html_url":"https://github.com/markovmodel/decomposed_msms","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/markovmodel/decomposed_msms","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/markovmodel%2Fdecomposed_msms","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/markovmodel%2Fdecomposed_msms/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/markovmodel%2Fdecomposed_msms/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/markovmodel%2Fdecomposed_msms/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/markovmodel","download_url":"https://codeload.github.com/markovmodel/decomposed_msms/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/markovmodel%2Fdecomposed_msms/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32339326,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-26T23:26:28.701Z","status":"online","status_checked_at":"2026-04-27T02:00:06.769Z","response_time":128,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":"2024-11-18T16:17:14.886Z","updated_at":"2026-04-27T14:05:06.401Z","avatar_url":"https://github.com/markovmodel.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Independent Markov decomposition\nThis repository contains code to reproduce numerical simulations and visualizations of\nTim Hempel, Mauricio J. del Razo, Christopher T. Lee, Bryn C. Taylor, Rommie E. Amaro, and Frank Noé:\n*Independent Markov Decomposition: Toward Modeling Kinetics of Biomolecular Complexes*,\nProc Natl Acad Sci USA 2021, 118 (31), e2105230118. https://doi.org/10.1073/pnas.2105230118.\n\n(Pre-print version: https://www.biorxiv.org/content/10.1101/2021.03.24.436806v1)\n\n## Overview\n### Fig1-scaling-multiple-3state-systems.ipynb\nDemonstrates combinatorial explosion of global states vs. independent Markov decomposition. Reproduces Fig. 1 in the manuscript.\n\n### Fig3cd-ion-channel-discrete-model.ipynb\nImplementation of Hodgkin-Huxley potassium ion channel model and numerical simulation of the dynamics. Reproduces Fig. 3c and d in the manuscript.\n\n### Fig4cd-ion-channel-optimal-partition.ipynb\nImplementation of coupled ion channel dimer and numerical simulation of the dynamics at various coupling strenghts. \nReproduces Fig. 4 c and d in the manuscript.\n\n### Fig5a-syt-decomposition.ipynb\nDependency graph estimation and visualization for MD data of Synaptotagmin-C2A domain. Reproduces Fig. 5a in the manuscript.\n\n### FigS1-approximation-quality-2-2state-systems.ipynb\nAssessment of limited sampling effects using a simple toy model. Reproduces Fig. S1 in the supplemental material.\n\n### FigS3-counterexample-Chignolin.ipynb\nCounterexample to IMD with small peptide Chignolin (10 amino acids). Reproduces Fig. S3 in the supplemental material.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmarkovmodel%2Fdecomposed_msms","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmarkovmodel%2Fdecomposed_msms","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmarkovmodel%2Fdecomposed_msms/lists"}