New computational method for prediction of interacting protein loop regions

Flexible loop regions of proteins play a crucial role in many biological functions such as protein–ligand recognition, enzymatic catalysis, and protein–protein association. To date, most computational methods that predict the conformational states of loops only focus on individual loop regions. However, loop regions are often spatially in close proximity to one another and their mutual interactions stabilize their conformations. We have developed a new method, titled CorLps, capable of simultaneously predicting such interacting loop regions. First, an ensemble of individual loop conformations is generated for each loop region. The members of the individual ensembles are combined and are accepted or rejected based on a steric clash filter. After a subsequent side‐chain optimization step, the resulting conformations of the interacting loops are ranked by the statistical scoring function DFIRE that originated from protein structure prediction. Our results show that predicting interacting loops with CorLps is superior to sequential prediction of the two interacting loop regions, and our method is comparable in accuracy to single loop predictions. Furthermore, improved predictive accuracy of the top‐ranked solution is achieved for 12‐residue length loop regions by diversifying the initial pool of individual loop conformations using a quality threshold clustering algorithm. Proteins 2010. © 2010 Wiley‐Liss, Inc.