SkeleDock: A Web Application for Scaffold Docking in PlayMolecule

Abstract: SkeleDock is a scaffold docking algorithm which uses the structure of a protein-ligand complex as a template to model the binding mode of a chemically similar system. This algorithm was evaluated in the D3R Grand Challenge 4 pose prediction challenge, where it achieved competitive performance. Furthermore, we show that, if crystallized fragments of the target ligand are available, SkeleDock can outperform rDock docking software at predicting the binding mode. This article also addresses the capacity of this algorithm to model macrocycles and deal with scaffold hopping. SkeleDock can be accessed at https://playmolecule.org/SkeleDock/.