One of the most pressing challenges in the post genomic era is the 
identification and characterization of protein-protein interactions (PPIs), as 
these are essential in understanding the cellular physiology of health and 
disease. Experimental techniques suitable for characterizing PPIs (X-ray 
crystallography or nuclear magnetic resonance spectroscopy, among others) are 
usually laborious, time-consuming and often difficult to apply to membrane 
proteins, and therefore require accurate prediction of the candidate interacting 
partners. High-throughput experimental methods (yeast two-hybrid and affinity 
purification) succumb to the same shortcomings, and can also lead to high rates 
of false positive and negative results. Therefore, reliable tools for predicting 
PPIs are needed. The use of the operon structure in the eukaryote Caenorhabditis 
elegans genome is a valuable, though underserved, tool for identifying 
physically or functionally interacting proteins. Based on the concept that genes 
organized in the same operon may encode physically or functionally related 
proteins, this algorithm is easy to be applied and, importantly, gives a limited 
number of candidate partners of a given protein, allowing for focused 
experimental verification. Moreover, this approach can be successfully used to 
predict PPIs in the human system, including those of membrane proteins.