(Q34207312)

31 July 2017

title

The efficiency of reactant site sampling in network-free simulation of rule-based models for biochemical systems (English)

1 reference

31 July 2017

William S Hlavacek

2

0 references

author name string

Jin Yang

series ordinal

1

1 reference

31 July 2017

publication date

10 August 2011

1 reference

31 July 2017

1 reference

31 July 2017

volume

8

1 reference

31 July 2017

issue

5

1 reference

31 July 2017

page(s)

055009

1 reference

Efficient modeling, simulation and coarse-graining of biological complexity with NFsim

31 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3168694

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28 July 2018

1 reference

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Modeling multivalent ligand-receptor interactions with steric constraints on configurations of cell-surface receptor aggregates

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3168694

Molecular machines or pleiomorphic ensembles: signaling complexes revisited

28 July 2018

1 reference

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A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3168694

Rule-based modeling of biochemical systems with BioNetGen

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3168694

Aggregation of membrane proteins by cytosolic cross-linkers: theory and simulation of the LAT-Grb2-SOS1 system

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3168694

Internal coarse-graining of molecular systems

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3168694

Simulation of large-scale rule-based models

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3168694

Kinetic Monte Carlo method for rule-based modeling of biochemical networks.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3168694

Programming with models: modularity and abstraction provide powerful capabilities for systems biology

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3168694

Trivalent antigens for degranulation of mast cells

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3168694

Stochastic simulation of chemical kinetics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3168694

Rules for modeling signal-transduction systems

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3168694

Automatic generation of cellular reaction networks with Moleculizer 1.0.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3168694

Mathematical and computational models of immune-receptor signalling

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3168694

The complexity of complexes in signal transduction.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3168694

Assembly of Cell Regulatory Systems Through Protein Interaction Domains

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3168694

Synthetic multivalent ligands in the exploration of cell-surface interactions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3168694

Signaling--2000 and beyond

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3168694

A thermodynamic model for receptor clustering

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3168694

Equilibrium theory for the clustering of bivalent cell surface receptors by trivalent ligands. Application to histamine release from basophils

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3168694

Transmembrane signaling: the joy of aggregation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3168694

BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3168694

Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3168694

Polyvalent Interactions in Biological Systems: Implications for Design and Use of Multivalent Ligands and Inhibitors

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21832806

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The kinetics of bivalent ligand-bivalent receptor aggregation: ring formation and the breakdown of the equivalent site approximation

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21832806

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1088/1478-3975/8/5/055009

1 reference

31 July 2017

1 reference

31 July 2017

1 reference