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

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TitleMeredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes.
Publication TypeJournal Article
Year of Publication2010
AuthorsTolle, DP, Le Novère, N
JournalBMC Syst Biol
Volume4
Pagination24
Date Published2010
ISSN1752-0509
KeywordsAlgorithms, Biopolymers, Computer Simulation, Diffusion, Models, Biological, Models, Chemical, Signal Transduction, Software
Abstract

<p><b>BACKGROUND: </b>Most cellular signal transduction mechanisms depend on a few molecular partners whose roles depend on their position and movement in relation to the input signal. This movement can follow various rules and take place in different compartments. Additionally, the molecules can form transient complexes. Complexation and signal transduction depend on the specific states partners and complexes adopt. Several spatial simulator have been developed to date, but none are able to model reaction-diffusion of realistic multi-state transient complexes.</p><p><b>RESULTS: </b>Meredys allows for the simulation of multi-component, multi-feature state molecular species in two and three dimensions. Several compartments can be defined with different diffusion and boundary properties. The software employs a Brownian dynamics engine to simulate reaction-diffusion systems at the reactive particle level, based on compartment properties, complex structure, and hydro-dynamic radii. Zeroth-, first-, and second order reactions are supported. The molecular complexes have realistic geometries. Reactive species can contain user-defined feature states which can modify reaction rates and outcome. Models are defined in a versatile NeuroML input file. The simulation volume can be split in subvolumes to speed up run-time.</p><p><b>CONCLUSIONS: </b>Meredys provides a powerful and versatile way to run accurate simulations of molecular and sub-cellular systems, that complement existing multi-agent simulation systems. Meredys is a Free Software and the source code is available at http://meredys.sourceforge.net/.</p>

DOI10.1186/1752-0509-4-24
Alternate JournalBMC Syst Biol
PubMed ID20233406
PubMed Central IDPMC2848630