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Rainer Pielot (Leibniz-Institute for Neurobiology, Magdeburg, Germany)Synapses are specialized cell-cell contacts between neurons of the central nervous system, which are characterized by highly specific networks of proteins at the synaptic membranes. The cytomatrix at the active zone (CAZ) is organizing at the presynaptic side the apparatus for the regulated release of transmitters. At the postsynaptic side the postsynaptic density (PSD) represents the machinery for detection, integration and transduction of the transmitter signal. The pre- and postsynaptic protein networks are the substrates for synaptic plasticity and are functionally regulated in their composition and modification of their components. These protein networks will be investigated by application of methods of bioinformatics and systems biology. The first step is the construction of a static interactom, i.e. the representation of the protein – interactions without considering the degree of modification. In a next step all static interactions will be replaced by ‘rules’, which describe the preconditions of a specific interaction. At this step it will be possible to construct dynamic protein networks for modeling of temporal processes of e.g. signal transduction. An a