Atomic coordinates were extracted from GPCRmd trajectories with MDtraj. Each trajectory was divided in sub-trajectories of a defined number of frames , f, and the mean, median, and SD of the x, y, z coordinates were calculated for each sub-trajectory. Additionally, atomic partial charges were generated for each atom in the system with RDkit Gasteiger charges calculator . The next steps are tailored for the two flavors of 3DDPDs generated: one-hot encoding residue specific (rs) 3DDPDs, and whole sequence embedding-like protein specific (ps) 3DDPDs (Figure ).