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arXiv · 2608.02525

On calculating polar solvation energy of nonrigid proteins in the Poisson-Boltzmann theory

Matthias Dogbatsey·Yuanzhen Shao·Emil Alexov·Shan Zhao
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Abstract

The Poisson-Boltzmann (PB) theory is a cornerstone of implicit solvent models for electrostatic analysis, and has found a great success in various biomolecular applications. However, in calculating polar solvation energy, one should consider that the structure of the protein changes upon transition from vacuum to water phases. To address this, here we report for the first time a generalized PB framework capable of accommodating nonrigid conformational changes without suffering from self-energy artifacts. For regularized PB models, in which the charge singularities are captured by the Green's functions, self-energies in the water and vacuum states will be analytically canceled. For non-regularized PB solvers, such as APBS and DelPhi, a simple thermodynamic cycle is proposed for nonrigid proteins by adding a Coulombic correction in vacuum. The generalized PB theory is validated using a perturbed two-atom system and a diverse set of proteins with different structures in vacuum and water, demonstrating its accuracy and robustness, regardless of the choice of sharp-interface and diffuse-interface PB models and different numerical solvers.

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Matthias Dogbatsey, Yuanzhen Shao, Emil Alexov, Shan Zhao. 2026-08-03. On calculating polar solvation energy of nonrigid proteins in the Poisson-Boltzmann theory. https://arxiv.org/abs/2608.02525

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