Leonard Harris
Last active: 2/5/2017

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

Chylek LA, Harris LA, Faeder JR, Hlavacek WS
Phys Biol. 2015 12 (4): 045007

PMID: 26178138 · PMCID: PMC4526164 · DOI:10.1088/1478-3975/12/4/045007

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.

MeSH Terms (5)

Computational Biology Models, Biological Models, Chemical Proteins Protein Structure, Tertiary

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