ArticleNature methods2011
Efficient modeling, simulation and coarse-graining of biological complexity with NFsim.
Article in Nature methods, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 134 papers.
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134 citing papers in PubMed.
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- Coupling Molecular and Cellular Dynamics in a Large-Scale Monte Carlo Simulation.International journal of molecular sciences · 2025Article
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- A Computational Protocol for the Knowledge-Based Assessment and Capture of Pathologies.Methods in molecular biology (Clifton, N.J.) · 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
- Visualizing mechanistic models by integrating site-specific molecular details into reaction networks.Frontiers in molecular biosciences · 2025Article
- A spatial model of autophosphorylation of CabioRxiv : the preprint server for biology · 2024Article
- Spleen Tyrosine Kinase (SYK) negatively regulates ITAM-mediated human NK cell signaling and CD19-CAR NK cell efficacy.bioRxiv : the preprint server for biology · 2024Article
- bnglViz: online visualization of rule-based models.Bioinformatics (Oxford, England) · 2024Article
- MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface.PLoS computational biology · 2024Article
- Article
- BioNetGMMFit: estimating parameters of a BioNetGen model from time-stamped snapshots of single cells.NPJ systems biology and applications · 2023Article
- kboolnet: a toolkit for the verification, validation, and visualization of reaction-contingency (rxncon) models.BMC bioinformatics · 2023Article
- MolClustPy: a Python package to characterize multivalent biomolecular clusters.Bioinformatics (Oxford, England) · 2023Article
- The maximum solubility product marks the threshold for condensation of multivalent biomolecules.Biophysical journal · 2023Article
- Verifiable biology.Journal of the Royal Society, Interface · 2023Review
- MolClustPy: A Python Package to Characterize Multivalent Biomolecular Clusters.bioRxiv : the preprint server for biology · 2023Article
- Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance.Molecular systems biology · 2023Article
- Targeted Quantification of Protein Phosphorylation and Its Contributions towards Mathematical Modeling of Signaling Pathways.Molecules (Basel, Switzerland) · 2023Review
74 more citing papers are in PubMed but not listed here.
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Managing the overwhelming numbers of molecular states and interactions is a fundamental obstacle to building predictive models of biological systems. Here we introduce the Network-Free Stochastic Simulator (NFsim), a general-purpose modeling platform that overcomes the combinatorial nature of molecular interactions. Unlike standard simulators that represent molecular species as variables in equations, NFsim uses a biologically intuitive representation: objects with binding and modification sites acted on by reaction rules. During simulations, rules operate directly on molecular objects to produce exact stochastic results with performance that scales independently of the reaction network size. Reaction rates can be defined as arbitrary functions of molecular states to provide powerful coarse-graining capabilities, for example to merge Boolean and kinetic representations of biological networks. NFsim enables researchers to simulate many biological systems that were previously inaccessible to general-purpose software, as we illustrate with models of immune system signaling, microbial signaling, cytoskeletal assembly and oscillating gene expression.
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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.