Calculate HDX intrinsic exchange rates.
Project description
Python package collection for HDX intrinsic exchange rate calculation. This package bundles existing implementations of this 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 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 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
Calculate instrinsic rate of amide hydrogen exchange in proteins.
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
PSX
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 <jhsmit@gmail.com> / <jochem.smit@kuleuven.be>
Project details
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