Study On Parallel Computational Approach To Protein Peptide Docking With Full Flexibility

Structural information related to protein-peptide complexes can be very useful fornovel drug discovery and design. The computational docking of protein and peptidecan supplement the structural information available on protein-peptide interactionsexplored by experimental ways. Generally,Protein-peptide docking method can bedescribed as three processes that occur in parallel: ab-initio peptide folding, peptidedocking with its receptor, and refnement of some fexible areas of the receptor as thepeptide is approaching. Several existing computational methods have been used tosample the degrees of freedom in the three processes, which are usually triggered in anorganized sequential scheme.Modeling fexibility of backbone is always a challenge of computational biologyfor protein docking. Most of existing docking methods are categorized semi-fexibledocking because of only considering fexible ligand. However, the receptor will producea conformational change, including the side chain motion, the backbone movement orother mutations when docking. First, we introduce a fexible docking method, whichexplicitly deals with fexible receptor areas. Second, we propose a parallel approachthat combines all the three processes during the docking of a folding peptide with afexible receptor. This parallel approach mimics the protein-peptide docking processin the real world.This paper uses many unbound protein-peptide docking cases to evaluate ourmethods. Our analysis of the results show that the explicit refnement of the fexibleareas of the receptor facilitated more accurate modeling of the interfaces of the com-plexes, while combining all of the moves in parallel helped the constructing of energyfunnels for predictions.