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Given two different protein-protein complexes our goal is to find the best way to superimpose them and to find out whether they share similar spatial physico-chemical binding patterns. To achieve this, we focus on protein-protein interfaces which are regions of interaction between two protein molecules. Two interfaces are considered to be similar, if the binding sites that comprise them share similar physico-chemical properties and shapes. Such interfaces may be created by proteins that have no sequence and fold similarity and algorithmically, we are facing the problem of labeled spatial pattern detection.