Vol.4 No.2 (June 2014)
Global Docking Method for Flexible Peptide Segment-Protein Interactions
Protein-peptide binding plays various important roles in living cells. In many cases, the peptide- binding sites of proteins are not known in prior. Then, computational prediction of the peptide- binding sites is desirable. Popular programs for protein-peptide docking usually depend strongly on the initial positions of peptides, such as Rosetta. To overcome this limitation, here we develop a global docking approach in which the peptide is initially distributed evenly on 26 surface locations of a virtual sphere around the protein, and define a selection parameter for discriminating native-like binding site from non-native sites. We used this approach to predict the native-like binding conformations of peptide-protein complexes, and in most cases the peptide-binding sites were correctly predicted, with Cα-RMSDs below 5.5 Å with respect to the crystal structures of peptides. The results of this study suggested that our approach may be very useful for the identification of peptide-binding sites of proteins.
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