SkeleDock: A Web Application for Scaffold Docking in PlayMolecule

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 then SkeleDock can outperform
rDock docking software at predicting the binding mode. This Application
Note also addresses the capacity of this algorithm to model macrocycles
and deal with scaffold hopping. SkeleDock can be accessed at https://playmolecule.org/SkeleDock/.