dxTuber: Detecting protein cavities, tunnels and clefts based on protein and solvent dynamics

► We developed a cavity detection method that fully accounts for protein dynamics. ► MD simulations are used to sample protein cavities by solvent molecules. ► Cavities are described as regions of high solvent residence probability. ► Our method is suitable for isolated cavities, tunnels and surface clefts. ► Cavities can be exported as individually selectable objects in PDB format. ► For each cavity total volume and profiles of cross-sectional area can be calculated.