https://github.com/jhsmit/hdxrate

Calculate protein amide hydrogen exchange rate
https://github.com/jhsmit/hdxrate

hdx-ms

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Calculate protein amide hydrogen exchange rate

• Host: GitHub
• URL: https://github.com/jhsmit/hdxrate
• Owner: Jhsmit
• License: gpl-3.0
• Created: 2020-11-02T11:48:52.000Z (about 4 years ago)
• Default Branch: master
• Last Pushed: 2024-07-25T15:13:43.000Z (4 months ago)
• Last Synced: 2024-10-05T00:13:38.045Z (about 2 months ago)
• Topics: hdx-ms
• Language: Python
• Homepage:
• Size: 354 KB
• Stars: 3
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.rst
  • Changelog: HISTORY.rst
  • Contributing: CONTRIBUTING.rst
  • License: LICENSE
  • Authors: AUTHORS.rst

Awesome Lists containing this project

README

        
=======

HDXrate

=======

.. image:: https://img.shields.io/pypi/v/hdxrate.svg

        :target: https://pypi.python.org/pypi/hdxrate

.. image:: https://readthedocs.org/projects/hdxrate/badge/?version=latest

        :target: https://hdxrate.readthedocs.io/en/latest/?badge=latest

        :alt: Documentation Status

.. image:: https://zenodo.org/badge/309354423.svg

   :target: https://zenodo.org/badge/latestdoi/309354423

Python package for HDX intrinsic exchange rate calculation. 

.. raw:: html

    

The calculations are based on the following papers:

  Bai, Y., Milne, J. S., Mayne, L. & Englander, S. W. Primary structure effects on peptide group hydrogen exchange. `Proteins Structure, Function, and Bioinformatics `__ 17, 75–86 (1993)

  Connelly, G. P., Bai, Y., Jeng, M.-F. & Englander, S. W. Isotope effects in peptide group hydrogen exchange. `Proteins `__ 17, 87–92 (1993).

  Mori, S., Zijl, P. C. M. van & 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 `__ 28, 325–332 (1997)

  

  Nguyen, D., Mayne, L., Phillips, M. C. & Walter Englander, S. Reference Parameters for Protein Hydrogen Exchange Rates. `J. Am. Soc. Mass Spectrom.  `__ 29, 1936–1939 (2018).

..

   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).

See also the excel sheet on the Englander group website: http://hx2.med.upenn.edu/download.html

* Free software: GNU General Public License v3

Features

--------

Calculate intrinsic rate of amide hydrogen exchange in proteins.

Installation

------------

::

   $ pip install hdxrate

or

::

   $ conda install -c conda-forge hdxrate

Usage

-----

::

   >>> from hdxrate import k_int_from_sequence

   >>> k_int_from_sequence('HHHHH', 300, 7.)

   array([0.00000000e+00, 2.62430718e+03, 6.29527446e+01, 6.29527446e+01,

       9.97734191e-01])

Credits

-------

HDXrate implementation is based on PSX intrinsic rate calculation

https://github.com/Niels-Bohr-Institute-XNS-StructBiophys/PSX

 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 `__ 52, 1427–1436 (2019).

Maintenance

```````````

* Jochem Smit  /