Extending the Calculus of Looping Sequences to model protein interaction at the domain level

Abstract

In previous papers we introduced a formalism, called Calculus of Looping Sequences (CLS), for describing biological systems and their evolution. CLS is based on term rewriting. Terms can be constructed by composing symbols of a given alphabet in sequences, which could be closed (looping) and contain other terms. In this paper we extend CLS to represent protein interaction at the domain level. Such an extension, called Calculus of Linked Looping Sequences (LCLS), is obtained by labeling alphabet symbols used in terms. Two symbols with the same label are considered to be linked. We introduce a type system to express a concept of well-formedness of LCLS terms, we give an operational semantics of the new calculus, and we show the application of LCLS to the description of a biological system. © Springer-Verlag Berlin Heidelberg 2007.