On delivering polar solvation free energy of proteins from energy minimized structures using a regularized super-Gaussian Poisson-Boltzmann model.

ABSTRACT: The biomolecules interact with their partners in an aqueous media; thus, their solvation energy is an important thermodynamics quantity. In previous works (J. Chem. Theory Comput. 14(2): 1020-1032), we demonstrated that the Poisson-Boltzmann (PB) approach reproduces solvation energy calculated via thermodynamic integration (TI) protocol if the structures of proteins are kept rigid. However, proteins are not rigid bodies and computing their solvation energy must account for their flexibility. Typically, in the framework of PB calculations, this is done by collecting snapshots from molecular dynamics (MD) simulations, computing their solvation energies, and averaging to obtain the ensemble-averaged solvation energy, which is computationally demanding. To reduce the computational cost, we hav

SUBMITTER: Panday SK 

PROVIDER: S-EPMC11586710 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature