Metadata-Version: 2.1
Name: HDXrate
Version: 0.1.0
Summary: Calculate HDX intrinsic exchange rates.
Home-page: https://github.com/Jhsmit/HDXrate
Author: Jochem Smit
Author-email: jhmit@gmail.com
License: GNU GPL
Keywords: HDX-MS,exchange rate
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Requires-Python: >=3.6
Requires-Dist: numpy

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HDXrate
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.. image:: https://img.shields.io/pypi/v/hdxrate.svg
        :target: https://pypi.python.org/pypi/hdxrate

.. image:: https://img.shields.io/travis/Jhsmit/hdxrate.svg
        :target: https://travis-ci.com/Jhsmit/hdxrate

.. image:: https://readthedocs.org/projects/hdxrate/badge/?version=latest
        :target: https://hdxrate.readthedocs.io/en/latest/?badge=latest
        :alt: Documentation Status




Python package collection for HDX intrinsic exchange rate calculation. This package bundles two existing implementations of this calculation, exPfact and PSX.

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 <https://doi.org/10.1002/prot.340170110>`__ 17, 75–86 (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 <https://doi.org/10.1002/(SICI)1097-0134(199707)28:3%3C325::AID-PROT3%3E3.0.CO;2-B>`__ 28, 325–332 (1997).

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
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Calculate instrinsic rate of amide hydrogen exchange in proteins.

Credits
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ExPfact
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https://github.com/skinnersp/exPfact

  Skinner, S. P., Radou, G., Tuma, R., Houwing-Duistermaat, J. J. & Paci, E. Estimating Constraints for Protection Factors from HDX-MS Data. `Biophysical Journal <https://doi.org/10.1016/j.bpj.2019.02.024>`__ 116, 1194–1203 (2019).


PSX
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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 <https://doi.org/10.1107/S1600576719012469/>`__ 52, 1427–1436 (2019).



Maintenance
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* Jochem Smit <jhsmit@gmail.com> / <jochem.smit@kuleuven.be>



