In this work, the MM/PB(GB)SA methods were tested on Protein-RNA complexes due the lack of a concrete scoring funtion specifically for these systems. The evaluations were made taking into account the minimized structures and MD trajectories; also, using an explicit and implicit solvent approach. Altought, repeatedly said, PB method is more rigorously than GB, the former is more sensitive to conformation sampling of the binding poses, that's why GB is a better approach both in predicting affinities and identifying near-native structures of protein-RNA systems.
In this work, the MM/PB(GB)SA methods were tested on Protein-RNA complexes due the lack of a concrete scoring funtion specifically for these systems. The evaluations were made taking into account the minimized structures and MD trajectories; also, using an explicit and implicit solvent approach. Altought, repeatedly said, PB method is more rigorously than GB, the former is more sensitive to conformation sampling of the binding poses, that's why GB is a better approach both in predicting affinities and identifying near-native structures of protein-RNA systems.