https://github.com/jhsmit/pyhdx

Derive ΔG for single residues from HDX-MS data
https://github.com/jhsmit/pyhdx

hdx-ms protein-dynamics protein-structure

Last synced: 21 days ago
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Derive ΔG for single residues from HDX-MS data

• Host: GitHub
• URL: https://github.com/jhsmit/pyhdx
• Owner: Jhsmit
• License: mit
• Created: 2019-09-06T10:37:06.000Z (about 5 years ago)
• Default Branch: master
• Last Pushed: 2024-10-14T16:07:18.000Z (about 1 month ago)
• Last Synced: 2024-10-16T04:41:04.934Z (about 1 month ago)
• Topics: hdx-ms, protein-dynamics, protein-structure
• Language: Jupyter Notebook
• Homepage: http://pyhdx.readthedocs.io
• Size: 46.6 MB
• Stars: 28
• Watchers: 3
• Forks: 12
• Open Issues: 59
• Metadata Files:
  • Readme: README.md
  • Changelog: HISTORY.rst
  • Contributing: CONTRIBUTING.rst
  • License: LICENSE.txt
  • Citation: CITATION.cff

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README

        
# PyHDX

[![zenodo](https://zenodo.org/badge/206772076.svg)](https://zenodo.org/badge/latestdoi/206772076)

[![biorxiv](https://img.shields.io/badge/bioRxiv-v2-%23be2635)](https://www.biorxiv.org/content/10.1101/2020.09.30.320887v2)

[![license](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)

[![docs](https://readthedocs.org/projects/pyhdx/badge/?version=latest)](https://pyhdx.readthedocs.io/en/latest/?badge=latest)

PyHDX is python project which can be used to derive Gibbs free energy from HDX-MS data.

[PyHDX web](http://pyhdx.jhsmit.org)

[PyHDX latest documentation](https://pyhdx.readthedocs.io/en/latest/)

[PyHDX on YouTube](https://www.youtube.com/channel/UCTro6Iv1BhvjUPYZNu5TJWg)

[![screenshot](images/screenshot_pyhdx043.png)](http://pyhdx.jhsmit.org/)

## Installation

Installation of the latest stable beta with `pip`:

```bash

$ pip install pyhdx

```

Installation with web interface extra:

```bash

$ pip install pyhdx[web]

```

Conda install (includes web interface extra):

```bash

$ conda install pyhdx

```

# Run PyHDX

Most up-to-date code examples are in the directory `pyhdx/templates`

To run the web server:

```bash

$ pyhdx serve

```

    

Please refer to the [docs](https://pyhdx.readthedocs.io/en/stable/) for more details on how to run PyHDX.

## Web Application

The PyHDX web application is currently hosted at:

http://pyhdx.jhsmit.org

A test file can be downloaded from [here](https://raw.githubusercontent.com/Jhsmit/PyHDX/master/tests/test_data/input/ecSecB_apo.csv) and [here](https://raw.githubusercontent.com/Jhsmit/PyHDX/master/tests/test_data/input/ecSecB_dimer.csv>) (right click, save as).

A beta version might be available at:

http://pyhdx-beta.jhsmit.org

## Publication

Our Analytical Chemistry Publication describing PyHDX can be found [here](https://doi.org/10.1021/acs.analchem.1c02155)

The latest version (v2) of our biorxiv paper: https://doi.org/10.1101/2020.09.30.320887 

Python code for analysis and generation the figures in the paper are here: https://github.com/Jhsmit/PyHDX-paper

## Other

HDX MS datasets repository and format:

https://github.com/Jhsmit/HDX-MS-datasets

HDXMS datasets python bindings:

https://github.com/Jhsmit/hdxms-datasets