Abstract: This invention relates to the prediction of protein sequence interactions. A method and apparatus are described for discovering rules of protein sequence interactions using a machine learning approach. The system uses a database of known protein sequence interactions, an algorithm to asses predictive quality of rules on one or more subsets of a protein sequence interaction database and a technique for generating new rule sets for testing. The system aims to optimise a rule set (descriptors of protein sequence interactions) against one or more predetermined criteria. One or more pairs of protein sequences which are likely to interact are generated according to the rule sets thus generated.