Docking and scoring: applications to drug discovery in the interactomics era

Background: Computational approaches such as docking and scoring are becoming routine in drug discovery as a complement to other more traditional techniques. However, so far, computer drug design methods have been applied to inhibit the function of individual proteins, and there is little available data on the use of these computational techniques to target protein-protein interactions. Objective: To establish a strategy for the use of current computational tools in drug discovery targeting protein-protein interactions. Method: Individual techniques applied to specific cases could be studied to derive a general strategy for targeting protein-protein interactions. Conclusion: Protein docking, interface prediction and hot-spot identification can contribute to the discovery of small molecule inhibitors targeting protein interactions of therapeutic interest, especially when little structural information is available.