Literature DB >> 11395441

STOCHSIM: modelling of stochastic biomolecular processes.

N Le Novère1, T S Shimizu.   

Abstract

SUMMARY: STOCHSIM is a stochastic simulator for chemical reactions. Molecules are represented as individual software objects that react according to probabilities derived from concentrations and rate constants. Version 1.2 of STOCHSIM provides a novel cross-platform graphical interface written in Perl/Tk. A simple two-dimensional spatial structure has also been implemented, in which nearest-neighbour interactions of molecules in a 2-D lattice can be simulated.

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Year:  2001        PMID： 11395441     DOI： 10.1093/bioinformatics/17.6.575

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  44 in total

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4.  Signaling through receptors and scaffolds: independent interactions reduce combinatorial complexity.

Authors:  Nikolay M Borisov; Nick I Markevich; Jan B Hoek; Boris N Kholodenko
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5.  Rate and extent of protein localization is controlled by peptide-binding domain association kinetics and morphology.

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Journal:  Protein Sci       Date:  2009-06       Impact factor: 6.725

6.  Simulation of large-scale rule-based models.

Authors:  Joshua Colvin; Michael I Monine; James R Faeder; William S Hlavacek; Daniel D Von Hoff; Richard G Posner
Journal:  Bioinformatics       Date:  2009-02-11       Impact factor: 6.937

7.  Biochemical simulations: stochastic, approximate stochastic and hybrid approaches.

Authors:  Jürgen Pahle
Journal:  Brief Bioinform       Date:  2009-01-16       Impact factor: 11.622

Review 8.  Systems biophysics of gene expression.

Authors:  Jose M G Vilar; Leonor Saiz
Journal:  Biophys J       Date:  2013-06-18       Impact factor: 4.033

9.  Simulated de novo assembly of golgi compartments by selective cargo capture during vesicle budding and targeted vesicle fusion.

Authors:  Haijun Gong; Debrup Sengupta; Adam D Linstedt; Russell Schwartz
Journal:  Biophys J       Date:  2008-05-09       Impact factor: 4.033

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

Authors:  Jin Yang; Michael I Monine; James R Faeder; William S Hlavacek
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2008-09-10
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