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November 20, 2025Communications ChemistryOpen Access

Accurate predictions of protein mutational effects accelerated with a hybrid-topology free energy protocol

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Authors

LKLucien KoenekoopNBNadine van de BrugWJWillem Jespers

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Overview

QresFEP-2 improves prediction accuracy of protein mutational effects in stability, binding, and interactions.

Key Points

  • The study aims to enhance prediction accuracy of protein mutational effects using a hybrid-topology FEP approach.
  • Developed QresFEP-2, a hybrid-topology free energy perturbation protocol.
  • Validated on a dataset with 10 protein systems and nearly 600 mutations.
  • Assessed thermodynamic stability through comprehensive domain-wide mutagenesis.
  • Evaluated site-directed mutagenesis effects on protein-ligand binding and protein-protein interactions.
  • Demonstrated superior accuracy and computational efficiency of QresFEP-2 compared to existing FEP protocols.
  • Validated efficacy across over 400 mutations in the B1 domain of streptococcal protein G.
  • Showed the applicability of QresFEP-2 in studying binding and interaction involving various proteins.

Cite This Study

Koenekoop et al. (2025) studied this question.

synapsesocial.com/papers/6924f074c0ce034ddc34fb3bhttps://doi.org/10.1038/s42004-025-01771-0
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