Improving the Accuracy of Implicit-Solvent Models with Physics-Based Molecular Surfaces

Dr. Nuo Wang
Department of Chemistry and Biochemistry, UC San Diego


Our variational implicit solvent model (VISM) improves upon the conventional implicit-solvent model by implementing a physical molecular surface that is generated from minimizing the free energy between the solute and the solvent. The free energy includes both the solute-solvent electrostatic and the van der Waals interactions, thus coupling the two types of interactions during the minimization process. Here we apply VISM to the calculation of the solvation free energy of realistic proteins. The VISM results are compared to both the conventional implicit-solvent and the molecular dynamics (MD) free energy perturbation results. It is shown that, without any parameter fitting, VISM solvation free energy is closer to that of MD comparing to the conventional implicit-solvent model.