title: The solvated interaction energy method for scoring binding affinities.
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.
authors.affiliation: Biotechnology Research Institute, National Research Council, Ottawa, ON, Canada.
authors.forename: Traian
authors.initials: T
authors.lastname: Sulea
authors.forename: Enrico O
authors.initials: EO
authors.lastname: Purisima
mesh_terms: D019295:Computational Biology / Q000379:methods*; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011506:Proteins / Q000378:metabolism*; D012997:Solvents / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D011506:Proteins; D012997:Solvents