New methods for reliable quantitative analysis of biological network data are in high demand in today’s
bioinformatics and systems biology. Here we demonstrate the applicability of the co-citation, developed earlier for the
analysis of scientific literature for finding functionally similar nodes in protein-protein interaction networks in several
model organisms. We prove the power of our approach in a novel way: the predicted closely related enzymes are
compared to the closeness of their enzyme commission (EC) numbers, therefore we can numerically evaluate our
prediction method. We have found clear correspondence between related enzymatic functions and high co-citation of
proteins in interaction networks.