======= HDXrate

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Python package for HDX intrinsic exchange rate calculation.

.. raw:: html

<img src="HDX_rate.jpg" width="400" height="400" alt="DALL-E generated image" align="center">

The calculations are based on the following papers:

'Englander xls sheets' 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).

'3ala' reference data: Stofella, M.; Seetaloo, N.; St John, A. N.; Paci, E.; Phillips, J. J.; Sobott, F. Recalibrating Protection Factors Using Millisecond Hydrogen/Deuterium Exchange Mass Spectrometry. Anal. Chem. 97 (5), 2648–2657 (2025).

pH correction: 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 sheets 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>