  One of the most difficult problems difficult problem in systems biology is to
discover protein-protein interactions as well as their associated functions.
The analysis and alignment of protein-protein interaction networks (PPIN),
which are the standard model to describe protein-protein interactions, has
become a key ingredient to obtain functional orthologs as well as evolutionary
conserved pathways and protein complexes. Several methods have been proposed to
solve the PPIN alignment problem, aimed to match conserved subnetworks or
functionally related proteins. However, the right balance between considering
network topology and biological information is one of the most difficult and
key points in any PPIN alignment algorithm which, unfortunately, remains
unsolved. Therefore, in this work, we propose AligNet, a new method and
software tool for the pairwise global alignment of PPIN that produces
biologically meaningful alignments and more efficient computations than
state-of-the-art methods and tools, by achieving a good balance between
structural matching and protein function conservation as well as reasonable
running times.
