Our covalent docking method (switch) follows the two-step mechanism of covalent inhibitors and was compared to non-covalent docking (non-cov ) and to covalent-only docking (cov-only). On the test set combining the CSKDE95 and CS244 sets (CSKDE304), the switch method performed better (success rate 79%) than cov-only (76%) and substantially better than non-cov (50%), demonstrating the advantage of focusing on non-covalent interactions in the sampling step and on the combination of non-covalent and covalent interactions in the scoring step. Using a distance cutoff to filter the poses before covalent docking saves computational time for a negligible success rate drop. Using a cutoff of 5 (76%) and 10 Å (79%) decreased the CPU time by 16 and 45%, respectively.