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Citing and Resources

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

  • Smit, J. H.; Krishnamurthy, S.; Srinivasu, B. Y.; Parakra, R.; Karamanou, S.; Economou, A. Probing Universal Protein Dynamics Using Hydrogen–Deuterium Exchange Mass Spectrometry-Derived Residue-Level Gibbs Free Energy. Anal. Chem. 2021, 93 (38), 12840–12847.

Citing dependencies

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

Intrinsic H/D exchange rates:

  • Bai, Y.; Milne, J. S.; Mayne, L.; Englander, S. W. Primary Structure Effects on Peptide Group Hydrogen Exchange. Proteins: Structure, Function, and Bioinformatics 1993, 17 (1), 75–86.
  • Connelly, G. P.; Bai, Y.; Jeng, M.-F.; Englander, S. W. Isotope Effects in Peptide Group Hydrogen Exchange. Proteins 1993, 17 (1), 87–92.
  • 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 1997, 28 (3), 325–332.<325::AID-PROT3>3.0.CO;2-B.
  • Nguyen, D.; Mayne, L.; Phillips, M. C.; Walter Englander, S. Reference Parameters for Protein Hydrogen Exchange Rates. J. Am. Soc. Mass Spectrom. 2018, 29 (9), 1936–1939.

See HDXrate for a python implementation of the Englander xls sheets for intrinsic exchange rate calculation.

MolStar protein viewer:

  • Sehnal, D.; Bittrich, S.; Deshpande, M.; Svobodová, R.; Berka, K.; Bazgier, V.; Velankar, S.; Burley, S. K.; Koča, J.; Rose, A. S. Mol Viewer: Modern Web App for 3D Visualization and Analysis of Large Biomolecular Structures. Nucleic Acids Research 2021*, 49 (W1), W431–W437.

Publications using PyHDX

  • Lin, X.; Haller, P.; Bavi, N.; Faruk, N.; Perozo, E.; Sosnick, T. R. Folding of Prestin’s Anion-Binding Site and the Mechanism of Outer Hair Cell Electromotility. eLife 2023, 12.
  • Bademosi, A. T.; Decet, M.; Kuenen, S.; Calatayud, C.; Swerts, J.; Gallego, S. F.; Schoovaerts, N.; Karamanou, S.; Louros, N.; Martin, E.; Sibarita, J.-B.; Vints, K.; Gounko, N. V.; Meunier, F. A.; Economou, A.; Versées, W.; Rousseau, F.; Schymkowitz, J.; Soukup, S.-F.; Verstreken, P. EndophilinA-Dependent Coupling between Activity-Induced Calcium Influx and Synaptic Autophagy Is Disrupted by a Parkinson-Risk Mutation. Neuron 2023.
  • Huang, J.; Chu, X.; Luo, Y.; Wang, Y.; Zhang, Y.; Zhang, Y.; Li, H. Insights into Phosphorylation-Induced Protein Allostery and Conformational Dynamics of Glycogen Phosphorylase via Integrative Structural Mass Spectrometry and In Silico Modeling. ACS Chem. Biol. 2022.
  • Krishnamurthy, S.; Eleftheriadis, N.; Karathanou, K.; Smit, J. H.; Portaliou, A. G.; Chatzi, K. E.; Karamanou, S.; Bondar, A.-N.; Gouridis, G.; Economou, A. A Nexus of Intrinsic Dynamics Underlies Translocase Priming. Structure 2021, 29 (8), 846-858.e7.
  • Yuan, B.; Portaliou, A. G.; Parakra, R.; Smit, J. H.; Wald, J.; Li, Y.; Srinivasu, B.; Loos, M. S.; Dhupar, H. S.; Fahrenkamp, D.; Kalodimos, C. G.; Duong van Hoa, F.; Cordes, T.; Karamanou, S.; Marlovits, T. C.; Economou, A. Structural Dynamics of the Functional Nonameric Type III Translocase Export Gate. Journal of Molecular Biology 2021, 433 (21), 167188.
  • Krishnamurthy, S.; Sardis, M.-F.; Eleftheriadis, N.; Chatzi, K. E.; Smit, J. H.; Karathanou, K.; Gouridis, G.; Portaliou, A. G.; Bondar, A.-N.; Karamanou, S.; Economou, A. Preproteins Couple the Intrinsic Dynamics of SecA to Its ATPase Cycle to Translocate via a Catch and Release Mechanism. Cell Reports 2022, 38 (6).
  • Smets, D.; Smit, J.; Xu, Y.; Karamanou, S.; Economou, A. Signal Peptide-Rheostat Dynamics Delay Secretory Preprotein Folding. Journal of Molecular Biology 2022, 434 (19), 167790.
  • Smets, D.; Tsirigotaki, A.; Smit, J. H.; Krishnamurthy, S.; Portaliou, A. G.; Vorobieva, A.; Vranken, W.; Karamanou, S.; Economou, A. Evolutionary Adaptation of the Protein Folding Pathway for Secretability. The EMBO Journal 2022, 41 (23), e111344.
  • Huang, J.; Chu, X.; Luo, Y.; Wang, Y.; Zhang, Y.; Zhang, Y.; Li, H. Insights into Phosphorylation-Induced Protein Allostery and Conformational Dynamics of Glycogen Phosphorylase via Integrative Structural Mass Spectrometry and In Silico Modeling. ACS Chem. Biol. 2022.

Publications citing PyHDX

  • Yu, J.; Uzuner, U.; Long, B.; Wang, Z.; Yuan, J. S.; Dai, S. Y. Artificial Intelligence-Based HDX (AI-HDX) Prediction Reveals Fundamental Characteristics to Protein Dynamics: Mechanisms on SARS-CoV-2 Immune Escape. iScience 2023, 26 (4), 106282.
  • Anderson, K. W.; Hudgens, J. W. Hydrophilic Interaction Liquid Chromatography at Subzero Temperature for Hydrogen–Deuterium Exchange Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2023, 34 (12), 2672–2679.
  • Largy, E.; Ranz, M. OligoR: A Native HDX/MS Data Processing Application Dedicated to Oligonucleotides. Anal. Chem. 2023, 95 (25), 9615–9622.
  • Uhrik, L.; Henek, T.; Planas-Iglesias, J.; Kucera, J.; Damborsky, J.; Marek, M.; Hernychova, L. Study of Protein Conformational Dynamics Using Hydrogen/Deuterium Exchange Mass Spectrometry. In Advanced Methods in Structural Biology; Sousa, Â., Passarinha, L., Eds.; Methods in Molecular Biology; Springer US: New York, NY, 2023; pp 293–318.
  • Vinciauskaite, V.; Masson, G. R. Fundamentals of HDX-MS. Essays in Biochemistry 2022, EBC20220111.
  • Stofella, M.; Skinner, S. P.; Sobott, F.; Houwing-Duistermaat, J.; Paci, E. High-Resolution Hydrogen–Deuterium Protection Factors from Sparse Mass Spectrometry Data Validated by Nuclear Magnetic Resonance Measurements. J. Am. Soc. Mass Spectrom. 2022, 33 (5), 813–822.
  • Zhang, W.; Xiang, Y.; Xu, W. Probing Protein Higher-Order Structures by Native Capillary Electrophoresis-Mass Spectrometry. TrAC Trends in Analytical Chemistry 2022, 157, 116739.


Other PyHDX resources:

General HDX-MS resources:

HDX-MS datasets: