The optimized rs3DDPD included "Rigidity" coordinate data calculated from 100-frame splits, where all atomic data was included for all residues in the protein sequence. In the atomic PCA, 95% of variability was kept and 5 PCs in the residue PCA. This resulted in a vector of 3,785 features for the class A GPCRdb MSA used, of length 757. The optimized ps3DDPD included all coordinate data statistics calculated from 100-frame splits, where all atomic data was included for all residues in the protein sequence and 95% of variability was kept in the atomic PCA. This resulted in a vector of 30 features.