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arXiv · 2509.19200

Dummy Atom Based Thermodynamic Integration Accurately Predicts Disulfide Redox Free Energies in Proteins

Daniel Mejia-Rodriguez·Suman Samantray·Margaret S. Cheung·Hoshin Kim
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Abstract

A thermodynamic integration (TI) protocol incorporating dummy atoms is introduced to calculate free energy differences for disulfide bond formation in proteins. This method successfully reproduces experimental redox potentials for multiple proteins, providing improved insights into the redox regulation of various proteins.

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Daniel Mejia-Rodriguez, Suman Samantray, Margaret S. Cheung, Hoshin Kim. 2025-09-23. Dummy Atom Based Thermodynamic Integration Accurately Predicts Disulfide Redox Free Energies in Proteins. https://arxiv.org/abs/2509.19200

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