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  • Title: The solvated interaction energy method for scoring binding affinities.
    Author: Sulea T, Purisima EO.
    Journal: Methods Mol Biol; 2012; 819():295-303. PubMed ID: 22183544.
    Abstract:
    The solvated interaction energy (SIE) is an end-point, physics-based scoring function for predicting ligand-binding affinities. It supplements the force-field interaction energy with the desolvation cost of binding. Parameters such as the solute dielectric constant, Born radii, a cavity term and an overall scaling coefficient and additive constant have been previously calibrated against a training set of 99 protein-ligand complexes. We describe the application of the method to estimating binding free energies from molecular dynamics trajectories of protein-ligand binding complexes.
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