Post-processing of Docking Results: Tools and Strategies

Abstract Obtaining ligand-receptor complexes is just the tip of the iceberg of the whole docking process. Various ligand orientations in the binding site of a protein are of limited application, if the energy of such complexes is not evaluated. Interactions occurring within such biological assemblies are most often assessed with the use of various scoring functions. There also exists a number of docking post-processing strategies, such as capturing of ligand-protein contacts in the form of interaction fingerprints (IFPs), followed by its statistical analysis. On the opposite pole of such automated strategies is a visual inspection of docking poses, which can be applied for small compound groups, but for obvious reasons cannot be used on a large scale. The chapter summarizes the strategies for evaluating ligand-protein complexes—from scoring functions, via IFPs analyzed using machine learning methods, to visual inspection. Attention is also given to hybrid approaches and comprehensive post-processing protocols that combine methods from various groups.