The PDB structures available in online databases often contain molecules and/or atoms that are not strictly related to the function of that protein. Such components must be removed before starting any calculation in order to streamline the procedures and avoid interference with the results. The manual deletion of unnecessary molecules becomes significantly expensive in terms of time as the number of structures to be prepared grows. We developed an algorithm called “PDB Cleaner of Original Elements” (PDB Cl.O.E.) to facilitate the cleaning procedure in case of large protein panels and provided this web tool to request clean protein structures. For more information about the procedure, please refer to: De Vita S., Lauro G., Ruggiero D., Terracciano S., Riccio R., and Bifulco G., J. Chem. Inf. Model., 2019, 59 (11), 4678-4690.