A Graph Grammar for Modelling RNA Folding

We propose a new approach for modelling the process of RNA folding as a graph transformation guided by the global value of free energy. Since the folding process evolves towards a configuration in which the free energy is minimal, the global behaviour resembles the one of a self-adaptive system. Each RNA configuration is a graph and the evolution of configurations is constrained by precise rules that can be described by a graph grammar.

[1]  Peter M. A. Sloot,et al.  Topological Characterization of Complex Systems: Using Persistent Entropy , 2015, Entropy.

[2]  Christoph Schaefer,et al.  Gene Expression with General Purpose Graph Rewriting Systems , 2009, Electron. Commun. Eur. Assoc. Softw. Sci. Technol..

[3]  Peter F. Stadler,et al.  RNA Secondary Structures , 2006 .

[4]  Michael Zuker,et al.  Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information , 1981, Nucleic Acids Res..

[5]  David Sankoff,et al.  RNA secondary structures and their prediction , 1984 .

[6]  Christoph A. Schaefer,et al.  Gene Expression with General Purpose Graph Rewriting Systems , 2009 .

[7]  Boris Böhlen.  Specific Graph Models and Their Mappings to a Common Model , 2003, AGTIVE.

[8]  K. Morris,et al.  The rise of regulatory RNA , 2014, Nature Reviews Genetics.

[9]  Ronny Lorenz,et al.  The Vienna RNA Websuite , 2008, Nucleic Acids Res..

[10]  I. Hofacker,et al.  Beyond energy minimization: approaches to the kinetic folding of RNA , 2008 .

[11]  Andrea Corradini,et al.  On the Concurrent Semantics of Algebraic Graph Grammars , 2005, Formal Methods in Software and Systems Modeling.

[12]  Christian M. Reidys,et al.  Topology and prediction of RNA pseudoknots , 2011, Bioinform..

[13]  Emanuela Merelli,et al.  Topology driven modeling: the IS metaphor , 2014, Natural Computing.

[14]  Reiko Heckel,et al.  Algebraic Approaches to Graph Transformation - Part II: Single Pushout Approach and Comparison with Double Pushout Approach , 1997, Handbook of Graph Grammars.

[15]  Reiko Heckel,et al.  Algebraic Approaches to Graph Transformation - Part I: Basic Concepts and Double Pushout Approach , 1997, Handbook of Graph Grammars.

[16]  Gj Dalenoort,et al.  LOGIC OF ARTIFICIAL LIFE: ABSTRACTING AND SYNTHESIZING THE PRINCIPLES OF LIVING SYSTEMS , 2004 .

[17]  P ? ? ? ? ? ? ? % ? ? ? ? , 1991 .

[18]  Arend Rensink.  The GROOVE Simulator: A Tool for State Space Generation , 2003, AGTIVE.

[19]  Nicola Paoletti,et al.  Adaptability checking in complex systems , 2016, Sci. Comput. Program..

[21]  P. Stadler,et al.  Graph Grammars as Models for the Evolution of Developmental Pathways , 2004 .

[22]  Sylvie Hamel,et al.  Modeling RNA tertiary structure motifs by graph-grammars , 2007, Nucleic acids research.