CMASA compare with sequence-based, global structure-based methods. A: The relationship between the CMASA RMSD and the global RMSD. B: The relationship between the CMASA RMSD and the sequence identity. C: The relationship between global RMSD and the sequence identity. 85 trypsins, 15 subtilisins and 30 random structures from the nrSCOP were selected for comparison. The CMASA_RMSD was calculated between 1mct active site (H57, D102 and S195) and the hits by the CMASA. The global_RMSD was calculated by CE package. Sequence identity was calculated from structure-based sequence alignment.