Given The RMSD and elapsed time of re-docking were evaluated and the results can be seen in Figure and Table . As shown in Figure , for Glide docking using ROCS results as starting conformation could slightly improve performance, in which, for eight structures, the RMSD of docked conformations of using ROCS is better than using The 6HAX (crystal structure of BAF ) system was taken as the example (as shown in Figure ). The running time of Glide and Vina were around 2 minutes. While the running time of PROTAC-INVENT is only 0.55 minutes. The RMSD of PROTAC-INVENT is 0.157, while those of Glide and Vina are much higher. These results demonstrate that the constrained docking protocol of PROTAC-INVENT is a better choice for doing PROTAC docking when it was hypothesized that a PROTAC may mimic a known PROTAC binding pose. Our approach performs better in this scenario due to two reasons: Firstly, it adopts a linker conformation to make sure two terminal warheads mimics those of template as close as possible; Secondly, the "local only" mode of Vina docking was used to fine tune the initial conformation so that the docking speed was greatly improved while the docking pose of PROTAC molecule can still fit with the binding pocket.