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The classified dataset can be used for two search applications. First, it can be searched with an interface of a newly determined complex to classify it and obtain hint for its function. Second, it can be searched with a complete protein. Here, for each representative of the created clusters we search the query protein for a region similar to either side of the interface. The binding partner of the selected region can potentially bind to the protein of interest. Applying the transformation of the alignment to the binding partner provides a prediction of its binding mode as would have been done by a docking algorithm. In this presentation I will focus on the first search type, which requires a simultaneous alignment between two sides of an interface and can not be performed by other methods.