Multi-state modeling of biomolecules (Q18145441)

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

RuleMonkey: software for stochastic simulation of rule-based models

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Structural analysis and stochastic modelling suggest a mechanism for calmodulin trapping by CaMKII

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Exact hybrid particle/population simulation of rule-based models of biochemical systems

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

COPASI--a COmplex PAthway SImulator

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Spatial rule-based modeling: a method and its application to the human mitotic kinetochore

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

A rule-based kinetic model of RNA polymerase II C-terminal domain phosphorylation

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Rule-based modeling and simulations of the inner kinetochore structure.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Programming biological models in Python using PySB

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Extracellular sheets and tunnels modulate glutamate diffusion in hippocampal neuropil

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

CaMKII activation and dynamics are independent of the holoenzyme structure: an infinite subunit holoenzyme approximation

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Cell polarity: quantitative modeling as a tool in cell biology

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Computational modeling of cellular signaling processes embedded into dynamic spatial contexts

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Rule-based multi-level modeling of cell biological systems

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Rule-based modelling and simulation of biochemical systems with molecular finite automata

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

CD4 and CD8 binding to MHC molecules primarily acts to enhance Lck delivery

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Rule-based spatial modeling with diffusing, geometrically constrained molecules

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

FAST MONTE CARLO SIMULATION METHODS FOR BIOLOGICAL REACTION-DIFFUSION SYSTEMS IN SOLUTION AND ON SURFACES.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Efficient stochastic simulation of reaction-diffusion processes via direct compilation

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Rule-based modeling of biochemical systems with BioNetGen

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Internal coarse-graining of molecular systems

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Simulation of large-scale rule-based models

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

PROMOT: modular modeling for systems biology

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Rules for modeling signal-transduction systems

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Structure of the autoinhibited kinase domain of CaMKII and SAXS analysis of the holoenzyme

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Automatic generation of cellular reaction networks with Moleculizer 1.0.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

How to impose microscopic reversibility in complex reaction mechanisms

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

The complexity of complexes in signal transduction.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Systems biology markup language: Level 2 and beyond

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

A spatially extended stochastic model of the bacterial chemotaxis signalling pathway

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Genomics. Molecular prodigality

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Binding and diffusion of CheR molecules within a cluster of membrane receptors

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Modelling cellular behaviour

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Miniature endplate current rise times less than 100 microseconds from improved dual recordings can be modeled with passive acetylcholine diffusion from a synaptic vesicle

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Protein molecules as computational elements in living cells

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Purification and characterization of a calmodulin-dependent protein kinase that is highly concentrated in brain

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

STOCHSIM: modelling of stochastic biomolecular processes.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201162

Exact stochastic simulation of coupled chemical reactions

30 May 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003844

Particle-Based Stochastic Simulation in Systems Biology

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003844

Rule-based modeling of biochemical networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003844

7 January 2021

Self-strengthening biphasic nanoparticle assemblies with intrinsic catch bonds

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003844

7 January 2021

Formal molecular biology

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003844

7 January 2021

Multi-level modelling via stochastic multi-level multiset rewriting

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003844

7 January 2021

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003844

1 reference

7 January 2021

10.1371/JOURNAL.PCBI.1003844

Identifiers

DOI

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1108703

DBLP publication ID

journals/ploscb/StefanBSK14

1 reference

DBLP Dataset 2021-01-02

OpenCitations bibliographic resource ID

28 January 2021

1108703

1 reference