HDXrate 0.1.1

Calculate HDX intrinsic exchange rates.

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 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.

Credits

ExPfact

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 116, 1194–1203 (2019).

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 <[e-mail]> / <[e-mail]>