In spite of the abundance of oligomeric proteins within a cell, the structural 
characterization of protein-protein interactions is still a challenging task. In 
particular, many of these interactions involve heteromeric complexes, which are 
relatively difficult to determine experimentally. Hence there is growing 
interest in using computational techniques to model such complexes. However, 
assembling large heteromeric complexes computationally is a highly combinatorial 
problem. Nonetheless the problem can be simplified greatly by considering 
interactions between protein trimers. After dimers and monomers, triangular 
trimers (i.e. trimers with pair-wise contacts between all three pairs of 
proteins) are the most frequently observed quaternary structural motifs 
according to the three-dimensional (3D) complex database. This article presents 
DockTrina, a novel protein docking method for modeling the 3D structures of 
nonsymmetrical triangular trimers. The method takes as input pair-wise contact 
predictions from a rigid body docking program. It then scans and scores all 
possible combinations of pairs of monomers using a very fast root mean square 
deviation test. Finally, it ranks the predictions using a scoring function which 
combines triples of pair-wise contact terms and a geometric clash penalty term. 
The overall approach takes less than 2 min per complex on a modern desktop 
computer. The method is tested and validated using a benchmark set of 220 bound 
and seven unbound protein trimer structures. DockTrina will be made available at 
http://nano-d.inrialpes.fr/software/docktrina.