3D-BLAST performance with E values on the protein query set SCOP-516. (a) The relationship between 3D-BLAST E values and the root mean square deviation (rmsd) values of aligned residues. The average rmsd values with E value below e-10, e-15, e-20, and e-25 are 3.57 Å, 2.85 Å, 2.37 Å and 2.25 Å, respectively, based on 22,415 protein structures randomly selected from the 516 returned lists. (b) The relationship between E values and the percentages of true (black) and false (gray) function assignment. The correct percentages of the superfamily assignments with E values below e-10, e-15, e-20 and e-25, are 95.26%, 97.67%, 99.31%, and 99.75%, respectively. The coverage values of the function assignment are 98.06% (<e-10), 91.47% (<e-15), 83.72% (<e-20), and 76.74 (<e-25).