“…Some of the limitations of structure-based HDX prediction models lie with inconsistencies in the molecular features that govern protection from HDX. These inconsistencies originate from the various types of conformational change that promote exchange, including global unfolding, subglobal motions intuitive interpretation, but weak correlation with HDX data, and challenges in defining SASA granularity hydrogen bonding 58,112,113,115,117 widely recognized as the main factor driving HDX protection, but not enough on its own to fully characterize protection electrostatic calculations 118,132,133,140 can explain the protection of solvent-accessible residues not involved in H-bonds, but force-field dependent and computationally intensive phenomenological expression [144][145][146][147][148]150 combines hydrogen bonding and atom burial; one of the most popular HDX prediction models, but can show poor correlation with HDX data combination of molecular features 55,[162][163][164]167,174 can involve nonstructural features (e.g., bond order, catalyst concentration, or hydrophobicity), but often just increases model complexity fractional-population models 55,107,172,179,180,182 estimate the free energy of exchange by calculating the probabilities of protected vs unprotected states, but very computationally intensive knowledge-based predictions 197,201,202,204 derive HDX protection directly from protein sequence, but usually show very weak correlation with HDX data between local minima, and breathing motions within minima. 58 The paradigm referred to as the fractional population model was proposed to circumvent difficulties associated with defining structure-based HDX prediction models.…”