3D dynamic protein descriptors (3DDPDs) were designed to capture the dynamic behavior of proteins in MD simulations. For this purpose, atomic coordinates were first extracted from the MD trajectories and their variability over a certain number of frames calculated. In order to account not only for the position but also for the type of atoms in the protein, atomic partial charges were computed. Next, two strategies were developed to condense the dense atomic information into protein descriptors (Figure ). These strategies correspond to the two types of 3DDPDs envisioned. The residue specific (rs)3DDPD is closer to classical one-hot encoded protein descriptors and defines each residue in the protein with a fixed number of features.