We present a novel partner-specific protein–protein interaction site prediction method called PAIRpred. PAIRpred uses information from both proteins in a protein complex to predict pairs of interacting residues from the two proteins using both sequence and structure information. PAIRpred presents a more detailed model of protein binding, and offers state of the art accuracy in predicting binding sites at the protein level as well as inter-protein residue contacts at the complex level. PAIRpred is available as a cloud based webserver. You can use it to make predictions for proteins of your interest.