First of all, the SMILES of linker was generated by REINVENT prior model and then merged with the supplied warhead pair (as part of the input) to form the SMILES of full PROTAC. Omega 26 program was then utilized to convert SMILES to a set of initial 3D conformations. The 3D conformations were then superimposed with the bound conformation of the reference PROTAC by using commercially available ROCS program . The ComboScore which is a weighted sum of shape and pharmacophore similarity was used to measure similarity between the reference conformer and the aligned conformation. Due to the large size of PROTAC, this superimposing is usually not able to create good alignment but still can serve the purpose of bringing the linker part of the PROTAC to the vicinity of the reference linker.