Energy-based modeling in BioNetGen

John A.P. Sekar, Justin S. Hogg, James R. Faeder

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

11 Scopus citations

Abstract

Biochemical processes typically operate on molecular sites (domains, motifs, residues). In rule-based modeling languages such as BioNetGen (BNG), reactions driven by the same set of sites with the same rate law can be represented using a single reaction rule. This leads to compact model representations when sites behave independently, but not when a large number of sites interact cooperatively. Additionally, loops of reactions are constrained by detailed balance equations involving their rate constants, but these constraints have to be enforced manually when specifying rate laws for rules. Here, we introduce the energy-based BioNetGen specification (eBNG), in which models always satisfy detailed balance and cooperative interactions are compactly specified as free energy contributions. We demonstrate this approach using well-known models of molecular cooperativity, such as ligand-induced receptor dimerization and allosteric modulation.

Original languageEnglish
Title of host publicationProceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016
EditorsKevin Burrage, Qian Zhu, Yunlong Liu, Tianhai Tian, Yadong Wang, Xiaohua Tony Hu, Qinghua Jiang, Jiangning Song, Shinichi Morishita, Kevin Burrage, Guohua Wang
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1460-1467
Number of pages8
ISBN (Electronic)9781509016105
DOIs
StatePublished - 17 Jan 2017
Event2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016 - Shenzhen, China
Duration: 15 Dec 201618 Dec 2016

Publication series

NameProceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016

Conference

Conference2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016
Country/TerritoryChina
CityShenzhen
Period15/12/1618/12/16

Keywords

  • Cooperativity
  • Detailed balance
  • Reaction network
  • Regulatory complexity
  • Rule-based modeling

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