T²F-Flex

T²F-Flex extends the functionality of T²F-Pharm and offers pharmacophore modeling from MD simulations of apo structures, i.e. empty binding sites, to represent the dynamic nature of the structures. Interaction hotspots on the grid are calculated per snapshot (subset of the trajectory) and subsequently clustered and summarized into a single pharmacophore model. This method allows to generate pharmacophores in the absence of ligand or interaction information and provides a feature-based description of protein binding sites.