ArticleJournal of the American Society for Mass Spectrometry2012
Quantitative assessment of protein structural models by comparison of H/D exchange MS data with exchange behavior accurately predicted by DXCOREX.
Article in Journal of the American Society for Mass Spectrometry, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 72 citations in OpenAlex.
- A machine learning method for calculating highly localized protein stabilities.Nature communications · 2026Article
- Site-resolved energetic information from HX-MS experiments.Nature chemical biology · 2026Article
- Inferring residue level hydrogen deuterium exchange with ReX.Communications chemistry · 2025Article
- The Ensemble Basis of Allostery and Function: Insights from Models of Local Unfolding.Journal of molecular biology · 2025Review
- Statistical Thermodynamics of the Protein Ensemble: Mediating Function and Evolution.Annual review of biophysics · 2025Review
- Impact of local unfolding fluctuations on the evolution of regional sequence preferences in proteins.Protein science : a publication of the Protein Society · 2025Article
- Interpretation of Hydrogen/Deuterium Exchange Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2024Article
- Mapping HDX-MS Data to Protein Conformations through Training Ensemble-Based Models.Journal of the American Society for Mass Spectrometry · 2023Article
- A cell-free antigen processing system informs HIV-1 epitope selection and vaccine design.The Journal of experimental medicine · 2023Article
- Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems.Chemical reviews · 2022Review
- A Thermodynamic Atlas of Proteomes Reveals Energetic Innovation across the Tree of Life.Molecular biology and evolution · 2022Article
- Prediction and Validation of a Protein's Free Energy Surface Using Hydrogen Exchange and (Importantly) Its Denaturant Dependence.Journal of chemical theory and computation · 2022Article
- Computational Structure Prediction for Antibody-Antigen Complexes From Hydrogen-Deuterium Exchange Mass Spectrometry: Challenges and Outlook.Frontiers in immunology · 2022Review
- Conserved allosteric ensembles in disordered proteins using TROSY/anti-TROSY RBiophysical journal · 2021Article
- Interpreting Hydrogen-Deuterium Exchange Experiments with Molecular Simulations: Tutorials and Applications of the HDXer Ensemble Reweighting Software [Article v1.0].Living journal of computational molecular science · 2021Article
- Hidden dynamic signatures drive substrate selectivity in the disordered phosphoproteome.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Interpretation of HDX Data by Maximum-Entropy Reweighting of Simulated Structural Ensembles.Biophysical journal · 2020Article
- Estimating Constraints for Protection Factors from HDX-MS Data.Biophysical journal · 2019Article
- Quantitative Evaluation of Native Protein Folds and Assemblies by Hydrogen Deuterium Exchange Mass Spectrometry (HDX-MS).Journal of the American Society for Mass Spectrometry · 2019Article
- POPPeT: a New Method to Predict the Protection Factor of Backbone Amide Hydrogens.Journal of the American Society for Mass Spectrometry · 2019Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
Peptide amide hydrogen/deuterium exchange mass spectrometry (DXMS) data are often used to qualitatively support models for protein structure. We have developed and validated a method (DXCOREX) by which exchange data can be used to quantitatively assess the accuracy of three-dimensional (3-D) models of protein structure. The method utilizes the COREX algorithm to predict a protein's amide hydrogen exchange rates by reference to a hypothesized structure, and these values are used to generate a virtual data set (deuteron incorporation per peptide) that can be quantitatively compared with the deuteration level of the peptide probes measured by hydrogen exchange experimentation. The accuracy of DXCOREX was established in studies performed with 13 proteins for which both high-resolution structures and experimental data were available. The DXCOREX-calculated and experimental data for each protein was highly correlated. We then employed correlation analysis of DXCOREX-calculated versus DXMS experimental data to assess the accuracy of a recently proposed structural model for the catalytic domain of a Ca(2+)-independent phospholipase A(2). The model's calculated exchange behavior was highly correlated with the experimental exchange results available for the protein, supporting the accuracy of the proposed model. This method of analysis will substantially increase the precision with which experimental hydrogen exchange data can help decipher challenging questions regarding protein structure and dynamics.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.