cramg
commented
3 years ago A strategic and systematically comparison between MM/PB(GB)SA methods using an extensive metal-free complexes dataset is presented, using Pearson correlation coefficient and Spearman ranking coefficient as evaluate guidelines. In general, the overall accuracy of MM/GBSA method is better than MM/PBSA, but the last is more sensitive at fold family level. Through the results, they argue why it is better to use these methods to calculate relative free energies rather than absolute free energies. Also, MM/PB(GB)SA methods works better when the ligand formal charge is neutral and on individual-fold-level. The best results were reached when a dielectric constant of 4 was used.
Sun, Huiyong, Youyong Li, Sheng Tian, Lei Xu, and Tingjun Hou. “Assessing the Performance of MM/PBSA and MM/GBSA Methods. 4. Accuracies of MM/PBSA and MM/GBSA Methodologies Evaluated by Various Simulation Protocols Using PDBbind Data Set.” Physical Chemistry Chemical Physics 16, no. 31 (2014): 16719–29.