The first step is a reversible process, while the second can be reversible or irreversible depending on the free energy profile of the reaction. To our knowledge, only CovDock takes this two-step mechanism into account by first performing a non-covalent docking of the ligand before forming the bond, while all other covalent docking algorithms directly link the ligand to the protein target. In this study, we aim at improving covalent docking by explicitly considering these two steps.