Citing and Resources#

When using PyHDX in your research, please cite our publication:

  • Jochem H. Smit, Srinath Krishnamurthy, Bindu Y. Srinivasu, Rinky Parakra, Spyridoula Karamanou, and Anastassios Economou. Probing Universal Protein Dynamics Using Hydrogen–Deuterium Exchange Mass Spectrometry-Derived Residue-Level Gibbs Free Energy. Analytical Chemistry, 93(38):12840–12847, September 2021. doi:10.1021/acs.analchem.1c02155.

Citing dependencies#

When using the different modules offered by PyHDX, please consider citing the following papers:

Intrinsic H/D exchange rates:

  • Yawen Bai, John S. Milne, Leland Mayne, and S. Walter Englander. Primary structure effects on peptide group hydrogen exchange. Proteins: Structure, Function, and Bioinformatics, 17(1):75–86, 1993. doi:10.1002/prot.340170110.

  • Gregory P. Connelly, Yawen Bai, Mei-Fen Jeng, and S. Walter Englander. Isotope effects in peptide group hydrogen exchange. Proteins: Structure, Function, and Genetics, 17(1):87–92, September 1993. doi:10.1002/prot.340170111.

  • Susumu Mori, Peter C. M. van Zijl, and David Shortle. 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(3):325–332, 1997. doi:10.1002/(SICI)1097-0134(199707)28:3<325::AID-PROT3>3.0.CO;2-B.

  • David Nguyen, Leland Mayne, Michael C. Phillips, and S. Walter Englander. Reference Parameters for Protein Hydrogen Exchange Rates. Journal of the American Society for Mass Spectrometry, 29(9):1936–1939, September 2018. doi:10.1021/jasms.8b05911.

PDBe MolStar protein viewer:

  • David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, and Alexander S Rose. Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Research, 49(W1):W431–W437, July 2021. doi:10.1093/nar/gkab314.

Publications using PyHDX#

The following publications use PyHDX:

  • Srinath Krishnamurthy, Nikolaos Eleftheriadis, Konstantina Karathanou, Jochem H. Smit, Athina G. Portaliou, Katerina E. Chatzi, Spyridoula Karamanou, Ana-Nicoleta Bondar, Giorgos Gouridis, and Anastassios Economou. A nexus of intrinsic dynamics underlies translocase priming. Structure, 29(8):846–858.e7, August 2021. doi:10.1016/j.str.2021.03.015.

  • Srinath Krishnamurthy, Marios-Frantzeskos Sardis, Nikolaos Eleftheriadis, Katerina E. Chatzi, Jochem H. Smit, Konstantina Karathanou, Giorgos Gouridis, Athina G. Portaliou, Ana-Nicoleta Bondar, Spyridoula Karamanou, and Anastassios Economou. Preproteins couple the intrinsic dynamics of SecA to its ATPase cycle to translocate via a catch and release mechanism. Cell Reports, February 2022. doi:10.1016/j.celrep.2022.110346.

  • Biao Yuan, Athina G. Portaliou, Rinky Parakra, Jochem H. Smit, Jiri Wald, Yichen Li, Bindu Srinivasu, Maria S. Loos, Harveer Singh Dhupar, Dirk Fahrenkamp, Charalampos G. Kalodimos, Franck Duong van Hoa, Thorben Cordes, Spyridoula Karamanou, Thomas C. Marlovits, and Anastassios Economou. Structural Dynamics of the Functional Nonameric Type III Translocase Export Gate. Journal of Molecular Biology, 433(21):167188, October 2021. doi:10.1016/j.jmb.2021.167188.

Resources#

Other PyHDX resources:

Paper code: https://github.com/Jhsmit/PyHDX-paper

BioRxiv v1: https://www.biorxiv.org/content/10.1101/2020.09.30.320887v1

BioRxiv v2: https://www.biorxiv.org/content/10.1101/2020.09.30.320887v2

General HDX-MS resources:

HDX-MS-resources: https://github.com/hadexversum/HDX-MS-resources

HDX-MS datasets (alpha):

HDX-MS-datasets: https://github.com/Jhsmit/HDX-MS-datasets