Abstract. In this paper, we present a rewriting framework for modeling molecular complexes, biochemical reaction rules, and generation of biochemical networks based on the representation of molecular complexes as a particular type of multigraphs with ports called molecular graphs. The advantage of this approach is to obtain for free a rewriting calculus which allows defining at the same level transformation rules and strategies for modeling rule selection and application, in order to prototype network generation. 1

c t i v it y e p o r t 2007 Table of contents

When modeling interactions between molecules or proteins, the behaviour of a protein is given by its functional domains that determine which other protein it can bind to or interact with and these domains are usually abstracted as sites that can be bound or free, visible or hidden. Hence a protein is characterized by the collection of interaction sites on its surface and proteins can bind to each other forming molecular complexes. Based on such structures, we considered port graphs [1] which are graphs with ports and with multiple edges and loops attached to ports of nodes. Molecular complexes are port graphs where each port is connected to at most one other port. Such restricted port graphs are called molecular graphs and their ports are called sites. We illustrate below a molecular graph G representing the initial state of the system modeling a fragment of the EGFR signaling cascade [12, 14]. The protagonists of this model are three types of proteins: the signal EGF, the receptor EGFR, and the adapter SHC. The molecular graph G ′ represents a state of the system where two signal proteins are already bound forming a dimer binding in turn a receptor. A node is graphically represent as a box with an unique identifier and a name placed outside the box. A site is represented as a filled, empty, or slashed circle on the surface of the box if its state is respectively bound, free, or hidden.