Supplementary data of "Ligand-induced Conformational Selection Predicts the Selectivity of Cysteine Protease Inhibitors" paper. This dataset consists of molecular dynamics simulations trajectories and topology of Cruzain, Cathepsin K and Cathepsin L enzymes in it apo form, together with validation simulations. We ran five replicate 100ns simulations on each complex, with randomized initial velocities.