Methods and systems for determining a set of control molecules for use in a combinatorial approach for the treatment of medical conditions, including providing one or more sets of control molecules, where each control molecule within the set acts on a set of targets and the number of control molecules within the one or more sets of control molecules is fewer than the number of targets within the sets of targets; and searching within the sets of control molecules to identify a subset of control molecules that together with a subset of targets form an artificial system to produce a biological effect through the modulation of the subset of targets.