Matthias Rarey

Today, structure-based design techniques like molecular docking and scoring are well-established computational approaches in the early phases of pharmaceutical research. Although de novo design methods were developed roughly 15 years ago, most methods applied today focus on the analysis of individual molecules. More recently, fragment-based approaches gain much popularity as the method of choice for finding new drugs. In this presentation, we will address the question of how computational methods can support this fragment-oriented approach.

The foundation of all methods is a formal description of chemical fragment spaces, which allow to model virtual synthesis. The fragment space represents the underlying search space for FlexNovo, a structure-based design tool, and ReCore for redesigning core fragments. Due to the complexity of fragment spaces, proper creation, visualization and navigation play an important role. Some new tools for these tasks together with sample spaces (generic and focussed) as well as test cases will be presented.