Figure 4

Comparison between DALI and RAPIDO on the dataset of human kinase structures. Every dot in the scatter plots represents one of the 2278 alignments between 68 structures (a) Length of the raw alignment provided by RAPIDO vs. the length of the corresponding DALI-alignment. Blue and red dots represent pairs of structures for which the RAPIDO alignment is significantly longer than the DALI alignment. Green and cyan dots indicated structures for which the rigid RMSD of the RAPIDO-alignment is substantially higher than that for the DALI-alignment or vice versa (Panel (c)). Data points surrounded by circles are discussed in the text. (b) Total number of residues assigned to rigid domains by RAPIDO vs. length of DALI alignment (c) Rigid RMSD for all atoms aligned by RAPIDO vs. rigid RMSD for atoms aligned by DALI. (d) Flexible RMSD for atom aligned and identified as belonging to rigid bodies by RAPIDO vs. rigid RMSD for all DALI-aligned atoms. Please note that the lengths and RMSDs given for the RAPIDO alignments correspond to aligned residues in Panels (a) and (c) while they correspond to rigid or structurally conserved residues in Panels (b) and (d); the difference between the two sets are flexible residues that have been aligned but are found in different conformations in the structures being compared.