Besides the economic importance of the disease, the rice-Xoo system serves as an excellent model for studying host-pathogen interactions because the genomes of both interacting partners are sequenced and there is considerable genetic variation in the host and pathogen.
The best scoring complexes were also used to identify key residues of both interacting partners, indicating that such an approach should help the design of more active and/or selective peptide blockers of targeted ion channels.
RNA-RNA binding occurs by formation of stacked intermolecular base pairs, which of course compete with the propensity of both interacting partners to form intramolecular base pairs.
When there is only one protein family member of both interacting partners in each species, one is guaranteed to get the correct alignment, assuming that it is a real complex in all organisms.
Adhesion can occur even at low temperatures or when the host cell cytoskeleton is blocked by the use of drugs, and the participation of molecules that are exposed on the surface of both interacting cells is very important to this process [ 31].
Our results, based on the inference of maximum-likelihood phylogenies, show that between pairs of interacting proteins, the evolutionary rates correlate, but the tree topologies of both interacting and non-interacting protein pairs are often dissimilar.
