We compared the performance of AC with the two state-of-the-art covalent docking algorithms of GOLD and AD (flexible side-chain method), using the combined set of 304 covalent complexes. With a success rate of 79%, AC clearly outperforms GOLD (68%) and AD (35%). Covalent docking with GOLD was fast and easy to set up, but special attention has to be paid to the atom types in the protein and ligand structure input files. Covalent docking with AD on the other hand required a substantial time investment for generating high-quality input files. The covalent docking success rate we obtained with GOLD was better than the one reported in a comparative benchmark study (68% vs. 53%), while the one for AD was substantially lower (35% vs. 55%). As the input files used in that study are not available, we do not know the underlying reasons for these differences.