Exploring the conformational diversity of loops on conserved frameworks

Loops are structurally variable regions, but the secondary structuralelements bracing loops are often conserved. Motifs with similarsecondary structures exist in the same and different proteinfamilies. In this study, we made an all-PDB-based analysis andproduced 495 motif families accessible from the Internet. Everymotif family contains some variable loops spanning a commonframework (a pair of secondary structures). The diversity ofloops and the convergence of frameworks were examined. In addition,we also identified 119 loops with conformational changes indifferent PDB files. These materials can give some directionsfor functional loop design and flexible docking.