Protein-Peptide Docking

Profacgen makes use of state-of-the-art docking software tools to model protein–peptide interactions and to predict the complex structure. The general modeling procedure is divided into two stages: (1) a global search is performed to predict the binding site at the protein receptor surface; (2) a flexible local docking method is used to fit the peptide structure into the known binding site. These two steps take into consideration the significant conformational changes upon binding of the two components. The peptide folding process is explicitly simulated in the docking protocol. When experimental or predicted data on binding site residues are available, such information can be used to constrain the docking to local regions of the protein surface. Finally, the best-scored structures are clustered, ranked and representatives of the largest clusters are selected for high resolution structural refinement before being presented to the customer.

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