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Simultaneous modeling of multiple loops in proteins

The most reliable methods for predicting protein structure are by way of homologous extension, using structural information from a closely related protein, or by “threading” through a set of predefined protein folds (“inverse folding”). Both sets of methods provide a model for the core of the protein —the structurally conserved secondary structures. Due to the large variability both in sequence and size of the loops that connect these secondary structures, they generally cannot be modeled using these techniques. Loop‐closure algorithms are aimed at predicting loop structures, given their end‐to‐end distance. Various such algorithms have been described, and all have been tested by predicting the structure of a single loop in a known protein. In this paper we propose a method, which is based on the bond‐scaling‐relaxation loop‐closure algorithm, for simultaneously predicting the structures of multiple loops, and demonstrate that, for two spatially close loops, simultaneous closure invariably leads to more accurate predictions than sequential closure. The accuracy of the predictions obtained for pairs of loops in the size range of 5–7 residues each is comparable to that obtained by other methods, when predicting the structures of single loops: the RMS deviations from the native conformations of various test cases modeled are approximately 0.6–1.7 Å for backbone atoms and 1.1–3.3 Å for all‐atoms.