A Biochemical Calculus Based on Strategic Graph Rewriting

Graphs are suitable for describing the structure of complex systems and graph transformations for modeling their dynamic evolution. We are interested in a particular representation of molecular complexes as graphs and of reaction patterns as graph transformations: • the behavior of a protein is given by its functional domains / sites on the surface • two proteins can interact by binding or changing the states of sites • bound proteins form complexes that have a graph-like structure •membranes can also form molecular complexes, called tissues