ArticleMethods in molecular biology (Clifton, N.J.)2019
MCell-R: A Particle-Resolution Network-Free Spatial Modeling Framework.
Article in Methods in molecular biology (Clifton, N.J.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Dynamic regulation of vesicle pools in a detailed spatial model of the complete synaptic vesicle cycle.Science advances · 2025Article
- A spatial model of autophosphorylation of CaMKII predicts that the lifetime of phospho-CaMKII after induction of synaptic plasticity is greatly prolonged by CaM-trapping.Frontiers in synaptic neuroscience · 2025Article
- A spatial model of autophosphorylation of CabioRxiv : the preprint server for biology · 2024Article
- MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface.PLoS computational biology · 2024Article
- A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0].Living journal of computational molecular science · 2023Article
- Stochastic model of ERK-mediated progesterone receptor translocation, clustering and transcriptional activity.Scientific reports · 2022Article
- WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications.Journal of chemical theory and computation · 2022Article
- Bayesian metamodeling of complex biological systems across varying representations.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- FluoSim: simulator of single molecule dynamics for fluorescence live-cell and super-resolution imaging of membrane proteins.Scientific reports · 2020Article
- Interactions between calmodulin and neurogranin govern the dynamics of CaMKII as a leaky integrator.PLoS computational biology · 2020Article
- Harnessing the Potential of Stem Cells for Disease Modeling: Progress and Promises.Journal of personalized medicine · 2020Review
- Article
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Authors and funding
7 authors.
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Abstract
Spatial heterogeneity can have dramatic effects on the biochemical networks that drive cell regulation and decision-making. For this reason, a number of methods have been developed to model spatial heterogeneity and incorporated into widely used modeling platforms. Unfortunately, the standard approaches for specifying and simulating chemical reaction networks become untenable when dealing with multistate, multicomponent systems that are characterized by combinatorial complexity. To address this issue, we developed MCell-R, a framework that extends the particle-based spatial Monte Carlo simulator, MCell, with the rule-based model specification and simulation capabilities provided by BioNetGen and NFsim. The BioNetGen syntax enables the specification of biomolecules as structured objects whose components can have different internal states that represent such features as covalent modification and conformation and which can bind components of other molecules to form molecular complexes. The network-free simulation algorithm used by NFsim enables efficient simulation of rule-based models even when the size of the network implied by the biochemical rules is too large to enumerate explicitly, which frequently occurs in detailed models of biochemical signaling. The result is a framework that can efficiently simulate systems characterized by combinatorial complexity at the level of spatially resolved individual molecules over biologically relevant time and length scales.
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Registered trials
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.