One-hot encoded rs3DDPDs performed significantly better than most of the other descriptors, except for PhysChem, with a Pearson r of 0.417 ± 0.004. Embedding-like ps3DDPDs, however, significantly outperformed all the other descriptors, including rs3DDPDs, with a Pearson r of 0.451 ± 0.003. These results were also confirmed in terms of Root Mean Square Error (RMSE), which was the lowest for ps3DDPDs (1.154 ± 0.003) and then QSAR models on average (1.168 ± 0.004), followed by rs3DDPDs (1.214 ± 0.005) and then the rest of nondynamic protein descriptors (from 1.124 ± 0.005 to 1.221 ± 0.006). A summary of all validation metrics is given in Table (random split) and Table (temporal split).