Hierarchical graphs for rule-based modeling of biochemical systems.
Background: In rule-based modeling, graphs are used to represent molecules: a colored vertex represents a component of a molecule, a vertex attribute represents the internal state of a component, and an edge represents a bond between components. Components of a molecule share the same color. Further...
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| Language: | English |
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Washington, D.C. : Oak Ridge, Tenn. :
United States. Department of Energy. Office of Science ; Distributed by the Office of Scientific and Technical Information, U.S. Department of Energy,
2011.
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MARC
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| 245 | 0 | 0 | |a Hierarchical graphs for rule-based modeling of biochemical systems. |
| 260 | |a Washington, D.C. : |b United States. Department of Energy. Office of Science ; |a Oak Ridge, Tenn. : |b Distributed by the Office of Scientific and Technical Information, U.S. Department of Energy, |c 2011. | ||
| 300 | |a Size: Article No. 45 : |b digital, PDF file. | ||
| 336 | |a text |b txt |2 rdacontent. | ||
| 337 | |a computer |b c |2 rdamedia. | ||
| 338 | |a online resource |b cr |2 rdacarrier. | ||
| 500 | |a Published through Scitech Connect. | ||
| 500 | |a 01/01/2011. | ||
| 500 | |a "Journal ID: ISSN 1471-2105." | ||
| 500 | |a "Other: PII: 1471-2105-12-45." | ||
| 500 | |a Lemons, Nathan W. ; Hu, Bin ; Hlavacek, William S. ; | ||
| 520 | 3 | |a Background: In rule-based modeling, graphs are used to represent molecules: a colored vertex represents a component of a molecule, a vertex attribute represents the internal state of a component, and an edge represents a bond between components. Components of a molecule share the same color. Furthermore, graph-rewriting rules are used to represent molecular interactions. A rule that specifies addition (removal) of an edge represents a class of association (dissociation) reactions, and a rule that specifies a change of a vertex attribute represents a class of reactions that affect the internal state of a molecular component. A set of rules comprises an executable model that can be used to determine, through various means, the system-level dynamics of molecular interactions in a biochemical system. Results: For purposes of model annotation, we propose the use of hierarchical graphs to represent structural relationships among components and subcomponents of molecules. We illustrate how hierarchical graphs can be used to naturally document the structural organization of the functional components and subcomponents of two proteins: the protein tyrosine kinase Lck and the T cell receptor (TCR) complex. We also show that computational methods developed for regular graphs can be applied to hierarchical graphs. In particular, we describe a generalization of Nauty, a graph isomorphism and canonical labeling algorithm. The generalized version of the Nauty procedure, which we call HNauty, can be used to assign canonical labels to hierarchical graphs or more generally to graphs with multiple edge types. The difference between the Nauty and HNauty procedures is minor, but for completeness, we provide an explanation of the entire HNauty algorithm. Conclusions: Hierarchical graphs provide more intuitive formal representations of proteins and other structured molecules with multiple functional components than do the regular graphs of current languages for specifying rule-based models, such as the BioNetGen language (BNGL). Thus, the proposed use of hierarchical graphs should promote clarity and better understanding of rule-based models. | |
| 536 | |b AC52-06NA25396. | ||
| 650 | 7 | |a 59 basic biological sciences |2 local. | |
| 650 | 7 | |a Biochemistry & molecular biology |2 local. | |
| 650 | 7 | |a Biotechnology & applied microbiology |2 local. | |
| 650 | 7 | |a Mathematical & computational biology |2 local. | |
| 710 | 2 | |a Los Alamos National Laboratory. |4 res. | |
| 710 | 2 | |a United States. Department of Energy. Office of Science. |4 spn. | |
| 710 | 1 | |a United States. |b Department of Energy. |b Office of Scientific and Technical Information |4 dst. | |
| 856 | 4 | 0 | |u https://www.osti.gov/servlets/purl/1626281 |z Full Text (via OSTI) |
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