Table 2

Aligning sequences according to MASIA motif analysis improves the correlation between structures.

The segmental RMSD between homologous motifs from huAPE1 (from PDB file 1DE9), DNase 1 (1DNK) and synaptojanin (I9Z) are shown first ungapped, from a simple alignment, and then gapped to match conserved residues (Motifs 1 and 2) and allow insertions in the secondary structure elements. Motif 12 is shown as an example of the RMSD where the molegos are spelled in a similar fashion in all three proteins.

Schein et al. BMC Bioinformatics 2002 3:37   doi:10.1186/1471-2105-3-37