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Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes
BACKGROUND: 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 transie...
Autores principales: | , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2010
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848630/ https://www.ncbi.nlm.nih.gov/pubmed/20233406 http://dx.doi.org/10.1186/1752-0509-4-24 |
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author | Tolle, Dominic P Le Novère, Nicolas |
author_facet | Tolle, Dominic P Le Novère, Nicolas |
author_sort | Tolle, Dominic P |
collection | PubMed |
description | BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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/. |
format | Text |
id | pubmed-2848630 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-28486302010-04-02 Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes Tolle, Dominic P Le Novère, Nicolas BMC Syst Biol Software BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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/. BioMed Central 2010-03-16 /pmc/articles/PMC2848630/ /pubmed/20233406 http://dx.doi.org/10.1186/1752-0509-4-24 Text en Copyright ©2010 Tolle and Le Novère; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Tolle, Dominic P Le Novère, Nicolas Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes |
title | Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes |
title_full | Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes |
title_fullStr | Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes |
title_full_unstemmed | Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes |
title_short | Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes |
title_sort | meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848630/ https://www.ncbi.nlm.nih.gov/pubmed/20233406 http://dx.doi.org/10.1186/1752-0509-4-24 |
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