Extending the calculus of looping sequences to model protein interaction at the domain level

Authors:
Roberto Barbuti;Andrea Maggiolo-Schettini;Paolo Milazzo
Affiliations:
Dipartimento di Informatica, Università di Pisa, Largo B. Pontecorvo, Pisa, Italy;Dipartimento di Informatica, Università di Pisa, Largo B. Pontecorvo, Pisa, Italy;Dipartimento di Informatica, Università di Pisa, Largo B. Pontecorvo, Pisa, Italy
Venue:
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
Year:
2007

Citing 7
Cited 7

Membrane Computing: An Introduction

Membrane Computing: An Introduction
Formal molecular biology

Theoretical Computer Science - Special issue: Computational systems biology
BioAmbients: an abstraction for biological compartments

Theoretical Computer Science - Special issue: Computational systems biology
A Calculus of Looping Sequences for Modelling Microbiological Systems

Fundamenta Informaticae - SPECIAL ISSUE ON CONCURRENCY SPECIFICATION AND PROGRAMMING (CS&P 2005) Ruciane-Nide, Poland, 28-30 September 2005
A Simple Calculus for Proteins and Cells

Electronic Notes in Theoretical Computer Science (ENTCS)
Bisimulation congruences in the calculus of looping sequences

ICTAC'06 Proceedings of the Third international conference on Theoretical Aspects of Computing
Brane calculi

CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology

Type Disciplines for Analysing Biologically Relevant Properties

Electronic Notes in Theoretical Computer Science (ENTCS)
Stochastic Calculus of Looping Sequences for the Modelling and Simulation of Cellular Pathways

Transactions on Computational Systems Biology IX
The calculus of looping sequences for modeling biological membranes

WMC'07 Proceedings of the 8th international conference on Membrane computing
The calculus of looping sequences

SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
A Formalism for the Description of Protein Interaction Dedicated to Jerzy Tiuryn on the Occasion of his 60th Birthday

Fundamenta Informaticae - From Mathematical Beauty to the Truth of Nature: to Jerzy Tiuryn on his 60th Birthday
Simulation techniques for the calculus of wrapped compartments

Theoretical Computer Science
Typed stochastic semantics for the calculus of looping sequences

Theoretical Computer Science

Quantified Score

Hi-index	0.00

Visualization

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.