A variety of experimental methods have been developed for the analysis of 
protein interactions. The majority of these methods either require disruption of 
the cells to detect molecular interactions or rely on indirect detection of the 
protein interaction. The bimolecular fluorescence complementation (BiFC) assay 
provides a direct approach for the visualization of molecular interactions in 
living cells and organisms. The BiFC approach is based on the facilitated 
association between two fragments of a fluorescent protein when the fragments 
are brought together by an interaction between proteins fused to the fragments. 
The BiFC approach has been used for visualization of interactions among a 
variety of structurally diverse interaction partners in many different cell 
types. It enables detection of transient complexes as well as complexes formed 
by a subpopulation of the interaction partners. It is essential to include 
negative controls in each experiment in which the interface between the 
interaction partners has been mutated or deleted. The BiFC assay has been 
adapted for simultaneous visualization of multiple protein complexes in the same 
cell and the competition for shared interaction partners. A ubiquitin-mediated 
fluorescence complementation assay has also been developed for visualization of 
the covalent modification of proteins by ubiquitin family peptides. These 
fluorescence complementation assays have a great potential to illuminate a 
variety of biological interactions in the future.