Molecular docking has been widely used in structure-based drug design to virtually screen large chemical libraries to predict the prefer... Show moreMolecular docking has been widely used in structure-based drug design to virtually screen large chemical libraries to predict the prefer conformations ligands that could bind the target site. Protein flexibility is a major issue that could be solved by ensemble docking which is docking to ‘ensemble’ of protein rigid conformations, such as snapshots obtained by molecular dynamics simulations. Our group has developed a method called ‘Efficiency of Stratification’ to evaluate a number of common snapshot selection strategies using a quality metric from stratified sampling (Xie et al. [19]). Docking was performed to four proteins and with each ligand numbers sets of up to five hundred ligands. In this paper, we generated distance matrices based on docking score to analysis the performance of the efficiency of stratification method. We observed that most docking score based score-based distance matrices have had better performance than structure-based distance matrices and with including any structure-based component overwhelms the docking-score component. Only a few ligands are required to get a good distance matrix. Show less
