Analysis, clustering and prediction of the conformation of short and medium size loops connecting regular secondary structures. Stephen D. Rufino, Luis E. Donate, Luc Canard and Tom L. Blundell.
Loops are regions of non-repetitive conformation connecting regular secondary structures.
While the core of a protein can be straight forwardly modelled from the structurally conserved regions of homologues of known structure, loops must be modelled from a selected homologue or from a loop chosen from outside the family. Here we present a loop prediction procedure that attempts to identify the conformational class of the loop rather than to select a specific loop from a database of fragments. Most of the previously described loop conformations were found among the populated classes. For each class a template was constructed containing both sequence preferences and the relative disposition of bounding secondary structures among member loops. During comparative modelling, the conformation of a loop can be predicted by identifying a loop class with which its sequence and disposition of bounding secondary structures are compatible.