{"id":19339495,"url":"https://github.com/becksteinlab/yiip_analysis","last_synced_at":"2026-05-15T17:38:19.350Z","repository":{"id":195683113,"uuid":"383897104","full_name":"Becksteinlab/yiip_analysis","owner":"Becksteinlab","description":"Analysis package for YiiP projects","archived":false,"fork":false,"pushed_at":"2023-10-16T14:15:26.000Z","size":1265,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-01-06T10:48:27.886Z","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":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Becksteinlab.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":"2021-07-07T18:53:08.000Z","updated_at":"2023-09-19T16:27:44.000Z","dependencies_parsed_at":null,"dependency_job_id":"fa838511-ffff-48dd-b75d-680065a7ec29","html_url":"https://github.com/Becksteinlab/yiip_analysis","commit_stats":null,"previous_names":["becksteinlab/yiip_analysis"],"tags_count":5,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2Fyiip_analysis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2Fyiip_analysis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2Fyiip_analysis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2Fyiip_analysis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Becksteinlab","download_url":"https://codeload.github.com/Becksteinlab/yiip_analysis/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240442511,"owners_count":19801914,"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":[],"created_at":"2024-11-10T03:22:29.056Z","updated_at":"2026-05-15T17:38:14.317Z","avatar_url":"https://github.com/Becksteinlab.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Code for \"Energy coupling and stoichiometry of Zn\u003csup\u003e2+\u003c/sup\u003e/H\u003csup\u003e+\u003c/sup\u003e antiport by the cation diffusion facilitator YiiP\"\n\n[![DOI](https://zenodo.org/badge/383897104.svg)](https://doi.org/10.5281/zenodo.8357619)\n\n\n\nThis repository contains code used for some of the computational aspects of the paper\n\n* Adel Hussein, Shujie Fan, Maria Lopez-Redondo, Ian Kenney, Xihui Zhang, Oliver Beckstein, and David L. Stokes. Energy coupling and stoichiometry of Zn\u003csup\u003e2+\u003c/sup\u003e/H\u003csup\u003e+\u003c/sup\u003e antiport by the cation diffusion facilitator YiiP. eLife, Apr 2023. doi: [10.7554/elife.87167](https://doi.org/10.7554/elife.87167)\n\nCode and data are archived: \n* Raw data files are archived in OSF project https://osf.io/r95qu (DOI [10.17605/OSF.IO/Y8BA2](https://doi.org/10.17605/OSF.IO/Y8BA2))\n* This GitHub code repository is archived in Zenodo under DOI [10.5281/zenodo.8357619](https://doi.org/10.5281/zenodo.8357619)\n\n## The following packages are required to use these scripts.\n* [NumPy](https://numpy.org/)\n* [SciPy](https://scipy.org/)\n* [Matplotlib](https://matplotlib.org/)\n* [MDAnalysis](https://www.mdanalysis.org/)\n* [tqdm](https://github.com/tqdm/tqdm)\n* [seaborn](https://seaborn.pydata.org/)\n* [pandas](https://pandas.pydata.org/)\n* [multibind](https://github.com/Becksteinlab/multibind)\n* [CpHMD-Analysis](https://gitlab.com/shenlab-amber-cphmd/cphmd-analysis) (see https://github.com/Hendejac/CpHMD-Analysis for the original `cphmdanalysis.py` script/module)\n\n## analysis\n`angle.py`, `rms.py`, and `R210_D72.py` are python scripts used to analyze equilibrium simulations, taking `md.gro` and `md[].xtc` as inputs, while the reference for this analysis is derived from the Protein Data Bank, accessible at https://www.rcsb.org/structure/5VRF.\n\n`cphmd.py` is the python script for analyzing CpHMD simulations, with `.log` and `.lamb` files as inputs.\n\n## MST inference\nThe folders `siteA` and `siteB` each contain scripts and corresponding example input data for performing MST inference on site A and site B, respectively. While the scripts themselves are identical for both site A and site B, the distinction lies in their input and output files.\n\n`monte_carlo.py` serves as the script responsible for executing a Monte Carlo process to refine the pKa values and binding free energies. It requires a `.csv` file that defines the states within the thermodynamic model, exemplified by `state.csv`, and an initial file, following the same format as `result.csv`. The `.csv` files located in the `target` folder as input data serves as the reference values for the Monte Carlo scheme. These files are reformatted experimental MST data, representing the data in Figure 4 of the paper.\n\n`analysis.ipynb` is a jupyter-notebook showing how to use the output of the monte_carlo process, `result.csv`, to generate the figures in `Figure 4 - figure supplement 5`, and `Figure 4 - figure supplement 6`.The `result.csv` files in `siteA` and `siteB` folders are reformatted versions of the supplementary data `figure4_figure-supplement5_source-data3.csv` and `figure4_figure-supplement6_source-data3.csv`, respectively.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecksteinlab%2Fyiip_analysis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbecksteinlab%2Fyiip_analysis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecksteinlab%2Fyiip_analysis/lists"}