We attempt to create a framework for predicting protein-protein interactions (PPI) that integrates structure-based information with other functional annotations, e.g. GO, co-expression and co-localization etc. Given two proteins with their sequences, the structure-based interaction prediction technique threads these two sequences to all the protein complexes in the PDB and then chooses the best potential match. Based on this match, logistic regression is used to evaluate the probability of these two proteins interacting. Experimental results indicate that the predictive power of the structure-based method is better than many other information sources. Also, combining the structure-based method with other information sources allows us to achieve a better performance than structure information is not used.