  Predicting protein-protein interactions from sequences is an important goal
of computational biology. Various sources of information can be used to this
end. Starting from the sequences of two interacting protein families, one can
use phylogeny or residue coevolution to infer which paralogs are specific
interaction partners within each species. We show that these two signals can be
combined to improve the performance of the inference of interaction partners
among paralogs. For this, we first align the sequence-similarity graphs of the
two families through simulated annealing, yielding a robust partial pairing. We
next use this partial pairing to seed a coevolution-based iterative pairing
algorithm. This combined method improves performance over either separate
method. The improvement obtained is striking in the difficult cases where the
average number of paralogs per species is large or where the total number of
sequences is modest.
