Another evaluation of the performance of MM/PBSA and MM/GBSA methods on protein-protein dataset is presented. Comparing the results of using distincts interior dielectric constant, minimization process and MD simulations showed interesting ideas. First, on relatively small protein-protein complexes, there wasn't a substantial improvement in the binding free energy predictions. Second, from the dielectric constant sampling, using the polar buried area (PBA) parameter of the interface complex may be a criterion to choose the optimal interior dielectric constant for MM/GBSA method.
Another evaluation of the performance of MM/PBSA and MM/GBSA methods on protein-protein dataset is presented. Comparing the results of using distincts interior dielectric constant, minimization process and MD simulations showed interesting ideas. First, on relatively small protein-protein complexes, there wasn't a substantial improvement in the binding free energy predictions. Second, from the dielectric constant sampling, using the polar buried area (PBA) parameter of the interface complex may be a criterion to choose the optimal interior dielectric constant for MM/GBSA method.