ArticleProceedings of the National Academy of Sciences of the United States of America2009
Internal coarse-graining of molecular systems.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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Who cites it
67 citing papers in PubMed.
- Quantitative modelling of P-TEFb mediated CTD phosphorylation identifies local cooperativity.PLoS computational biology · 2026Article
- Targeted Quantification of Protein Phosphorylation and Its Contributions towards Mathematical Modeling of Signaling Pathways.Molecules (Basel, Switzerland) · 2023Review
- Probabilistic Inference with Polymerizing Biochemical Circuits.Entropy (Basel, Switzerland) · 2022Article
- Comparison of rule- and ordinary differential equation-based dynamic model of DARPP-32 signalling network.PeerJ · 2022Article
- Crosstalk and ultrasensitivity in protein degradation pathways.PLoS computational biology · 2020Article
- Multi-scale stochastic organization-oriented coarse-graining exemplified on the human mitotic checkpoint.Scientific reports · 2019Article
- Chemoinformatics and structural bioinformatics in OCaml.Journal of cheminformatics · 2019Article
- Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor.PLoS computational biology · 2019Article
- Mechanistic Models of Cellular Signaling, Cytokine Crosstalk, and Cell-Cell Communication in Immunology.Frontiers in immunology · 2019Article
- Intrinsic limits of information transmission in biochemical signalling motifs.Interface focus · 2018Article
- Coarse-graining as a downward causation mechanism.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2017Review
- From word models to executable models of signaling networks using automated assembly.Molecular systems biology · 2017Article
- Maximal aggregation of polynomial dynamical systems.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Multivalent Molecules as Modulators of RNA Granule Size and Composition.Biophysical journal · 2017Article
- LASSIE: simulating large-scale models of biochemical systems on GPUs.BMC bioinformatics · 2017Article
- A strand graph semantics for DNA-based computation.Theoretical computer science · 2016Article
- Computational Modeling, Formal Analysis, and Tools for Systems Biology.PLoS computational biology · 2016Review
- Automated adaptive inference of phenomenological dynamical models.Nature communications · 2015Article
- Modeling for (physical) biologists: an introduction to the rule-based approach.Physical biology · 2015Review
- Analytical reduction of combinatorial complexity arising from multiple protein modification sites.Journal of the Royal Society, Interface · 2015Article
7 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
Modelers of molecular signaling networks must cope with the combinatorial explosion of protein states generated by posttranslational modifications and complex formation. Rule-based models provide a powerful alternative to approaches that require explicit enumeration of all possible molecular species of a system. Such models consist of formal rules stipulating the (partial) contexts wherein specific protein-protein interactions occur. These contexts specify molecular patterns that are usually less detailed than molecular species. Yet, the execution of rule-based dynamics requires stochastic simulation, which can be very costly. It thus appears desirable to convert a rule-based model into a reduced system of differential equations by exploiting the granularity at which rules specify interactions. We present a formal (and automated) method for constructing a coarse-grained and self-consistent dynamical system aimed at molecular patterns that are distinguishable by the dynamics of the original system as posited by the rules. The method is formally sound and never requires the execution of the rule-based model. The coarse-grained variables do not depend on the values of the rate constants appearing in the rules, and typically form a system of greatly reduced dimension that can be amenable to numerical integration and further model reduction techniques.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.