The interaction between proteins is an important feature of protein functions. Behind protein-protein interactions there are protein domains interacting with each others to perform the necessary functions. Therefore, understanding proteins interactions at the domain level gives a global view of the protein-protein interaction network. In this study, we employ the domain combination pair approach, introduced by Han et. al [Han et. al. 2004], to derive putative protein domain-domain interactions from the protein-protein interaction database DIP. Domain annotation of each protein-protein interaction record in DIP is obtained from the protein domain database, Pfam.The results of putative domain-domain interaction by Han et al. was extended to seven species (C.elegan, D.melanogaster, E.coli, H.pylori, H.sapiens, M.musculus and S.cerevisiae) and a combination of all seven species. For each case, a negative learning set (non-interacting protein sequences) is constructed in order to improve the accuracy of domain-domain interactions prediction. The predicted domain-domain interaction pairs and PIP results are available at http://210.70.80.163/kzbio2/.
