=======
HDXrate
=======
.. 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
.. image:: https://zenodo.org/badge/309354423.svg
:target: https://zenodo.org/badge/latestdoi/309354423
Python package for HDX intrinsic exchange rate calculation.
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)
Connelly, G. P., Bai, Y., Jeng, M.-F. & Englander, S. W. Isotope effects in peptide group hydrogen exchange. `Proteins <http://doi.wiley.com/10.1002/prot.340170111>`__ 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 <https://doi.org/10.1002/(SICI)1097-0134(199707)28:3%3C325::AID-PROT3%3E3.0.CO;2-B>`__ 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. <https://doi.org/10.1007/s13361-018-2021-z>`__ 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 <https://doi.org/10.1107/S1600576719012469/>`__ 52, 1427–1436 (2019).
Maintenance
```````````
* Jochem Smit <jhsmit@gmail.com> / <jochem.smit@kuleuven.be>
Raw data
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"description": "=======\r\nHDXrate\r\n=======\r\n\r\n\r\n.. image:: https://img.shields.io/pypi/v/hdxrate.svg\r\n :target: https://pypi.python.org/pypi/hdxrate\r\n\r\n.. image:: https://img.shields.io/travis/Jhsmit/hdxrate.svg\r\n :target: https://travis-ci.com/Jhsmit/hdxrate\r\n\r\n.. image:: https://readthedocs.org/projects/hdxrate/badge/?version=latest\r\n :target: https://hdxrate.readthedocs.io/en/latest/?badge=latest\r\n :alt: Documentation Status\r\n\r\n.. image:: https://zenodo.org/badge/309354423.svg\r\n :target: https://zenodo.org/badge/latestdoi/309354423\r\n\r\n\r\nPython package for HDX intrinsic exchange rate calculation. \r\nThe calculations are based on the following papers:\r\n\r\n 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\u201386 (1993)\r\n\r\n Connelly, G. P., Bai, Y., Jeng, M.-F. & Englander, S. W. Isotope effects in peptide group hydrogen exchange. `Proteins <http://doi.wiley.com/10.1002/prot.340170111>`__ 17, 87\u201392 (1993).\r\n\r\n\r\n Mori, S., Zijl, P. C. M. van & Shortle, D. Measurement of water\u2013amide 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\u2013332 (1997)\r\n \r\n Nguyen, D., Mayne, L., Phillips, M. C. & Walter Englander, S. Reference Parameters for Protein Hydrogen Exchange Rates. `J. Am. Soc. Mass Spectrom. <https://doi.org/10.1007/s13361-018-2021-z>`__ 29, 1936\u20131939 (2018).\r\n\r\n..\r\n 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\u20132750 (2017).\r\n\r\n\r\nSee also the excel sheet on the Englander group website: http://hx2.med.upenn.edu/download.html\r\n\r\n\r\n* Free software: GNU General Public License v3\r\n\r\n\r\nFeatures\r\n--------\r\n\r\nCalculate intrinsic rate of amide hydrogen exchange in proteins.\r\n\r\nInstallation\r\n------------\r\n\r\n::\r\n\r\n $ pip install hdxrate\r\n\r\nor\r\n\r\n::\r\n\r\n $ conda install -c conda-forge hdxrate\r\n\r\nUsage\r\n-----\r\n\r\n::\r\n\r\n >>> from hdxrate import k_int_from_sequence\r\n >>> k_int_from_sequence('HHHHH', 300, 7.)\r\n array([0.00000000e+00, 2.62430718e+03, 6.29527446e+01, 6.29527446e+01,\r\n 9.97734191e-01])\r\n\r\n\r\nCredits\r\n-------\r\n\r\nHDXrate implementation is based on PSX intrinsic rate calculation\r\nhttps://github.com/Niels-Bohr-Institute-XNS-StructBiophys/PSX\r\n\r\n Pedersen, M. C. et al. PSX, Protein\u2013Solvent 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\u20131436 (2019).\r\n\r\n\r\n\r\nMaintenance\r\n```````````\r\n\r\n* Jochem Smit <jhsmit@gmail.com> / <jochem.smit@kuleuven.be>\r\n\r\n",
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