Modeling for (physical) biologists: an introduction to the rule-based approach

Phys Biol. 2015 Jul 16;12(4):045007. doi: 10.1088/1478-3975/12/4/045007.

Abstract

Models that capture the chemical kinetics of cellular regulatory networks can be specified in terms of rules for biomolecular interactions. A rule defines a generalized reaction, meaning a reaction that permits multiple reactants, each capable of participating in a characteristic transformation and each possessing certain, specified properties, which may be local, such as the state of a particular site or domain of a protein. In other words, a rule defines a transformation and the properties that reactants must possess to participate in the transformation. A rule also provides a rate law. A rule-based approach to modeling enables consideration of mechanistic details at the level of functional sites of biomolecules and provides a facile and visual means for constructing computational models, which can be analyzed to study how system-level behaviors emerge from component interactions.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • Computational Biology*
  • Models, Biological*
  • Models, Chemical
  • Protein Structure, Tertiary*
  • Proteins / chemistry*

Substances

  • Proteins