Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software
<p>Abstract</p> <p>Background</p> <p>There is an increasing need for computer-generated models that can be used for explaining the emergence and predicting the behavior of multi-protein dynamic structures in cells. Multi-agent systems (MAS) have been proposed as good ca...
Main Authors: | , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
BMC
2005-09-01
|
Series: | BMC Bioinformatics |
Online Access: | http://www.biomedcentral.com/1471-2105/6/228 |
id |
doaj-20df12b734784cd5911a6d9d04a2686a |
---|---|
record_format |
Article |
spelling |
doaj-20df12b734784cd5911a6d9d04a2686a2020-11-25T01:03:10ZengBMCBMC Bioinformatics1471-21052005-09-016122810.1186/1471-2105-6-228Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based softwareBeslon GuillaumeGripon SébastienPerrin FrançoisRobardet CélineSoula HédiGandrillon Olivier<p>Abstract</p> <p>Background</p> <p>There is an increasing need for computer-generated models that can be used for explaining the emergence and predicting the behavior of multi-protein dynamic structures in cells. Multi-agent systems (MAS) have been proposed as good candidates to achieve this goal.</p> <p>Results</p> <p>We have created 3DSpi, a multi-agent based software that we used to explore the generation of multi-protein dynamic structures. Being based on a very restricted set of parameters, it is perfectly suited for exploring the minimal set of rules needed to generate large multi-protein structures. It can therefore be used to test the hypothesis that such structures are formed and maintained by principles of self-organization. We observed that multi-protein structures emerge and that the system behavior is very robust, in terms of the number and size of the structures generated. Furthermore, the generated structures very closely mimic spatial organization of real life multi-protein structures.</p> <p>Conclusion</p> <p>The behavior of 3DSpi confirms the considerable potential of MAS for modeling subcellular structures. It demonstrates that robust multi-protein structures can emerge using a restricted set of parameters and allows the exploration of the dynamics of such structures. A number of easy-to-implement modifications should make 3DSpi the virtual simulator of choice for scientists wishing to explore how topology interacts with time, to regulate the function of interacting proteins in living cells.</p> http://www.biomedcentral.com/1471-2105/6/228 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Beslon Guillaume Gripon Sébastien Perrin François Robardet Céline Soula Hédi Gandrillon Olivier |
spellingShingle |
Beslon Guillaume Gripon Sébastien Perrin François Robardet Céline Soula Hédi Gandrillon Olivier Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software BMC Bioinformatics |
author_facet |
Beslon Guillaume Gripon Sébastien Perrin François Robardet Céline Soula Hédi Gandrillon Olivier |
author_sort |
Beslon Guillaume |
title |
Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software |
title_short |
Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software |
title_full |
Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software |
title_fullStr |
Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software |
title_full_unstemmed |
Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software |
title_sort |
modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3dspi, a multi-agent-based software |
publisher |
BMC |
series |
BMC Bioinformatics |
issn |
1471-2105 |
publishDate |
2005-09-01 |
description |
<p>Abstract</p> <p>Background</p> <p>There is an increasing need for computer-generated models that can be used for explaining the emergence and predicting the behavior of multi-protein dynamic structures in cells. Multi-agent systems (MAS) have been proposed as good candidates to achieve this goal.</p> <p>Results</p> <p>We have created 3DSpi, a multi-agent based software that we used to explore the generation of multi-protein dynamic structures. Being based on a very restricted set of parameters, it is perfectly suited for exploring the minimal set of rules needed to generate large multi-protein structures. It can therefore be used to test the hypothesis that such structures are formed and maintained by principles of self-organization. We observed that multi-protein structures emerge and that the system behavior is very robust, in terms of the number and size of the structures generated. Furthermore, the generated structures very closely mimic spatial organization of real life multi-protein structures.</p> <p>Conclusion</p> <p>The behavior of 3DSpi confirms the considerable potential of MAS for modeling subcellular structures. It demonstrates that robust multi-protein structures can emerge using a restricted set of parameters and allows the exploration of the dynamics of such structures. A number of easy-to-implement modifications should make 3DSpi the virtual simulator of choice for scientists wishing to explore how topology interacts with time, to regulate the function of interacting proteins in living cells.</p> |
url |
http://www.biomedcentral.com/1471-2105/6/228 |
work_keys_str_mv |
AT beslonguillaume modelingtheemergenceofmultiproteindynamicstructuresbyprinciplesofselforganizationthroughtheuseof3dspiamultiagentbasedsoftware AT griponsebastien modelingtheemergenceofmultiproteindynamicstructuresbyprinciplesofselforganizationthroughtheuseof3dspiamultiagentbasedsoftware AT perrinfrancois modelingtheemergenceofmultiproteindynamicstructuresbyprinciplesofselforganizationthroughtheuseof3dspiamultiagentbasedsoftware AT robardetceline modelingtheemergenceofmultiproteindynamicstructuresbyprinciplesofselforganizationthroughtheuseof3dspiamultiagentbasedsoftware AT soulahedi modelingtheemergenceofmultiproteindynamicstructuresbyprinciplesofselforganizationthroughtheuseof3dspiamultiagentbasedsoftware AT gandrillonolivier modelingtheemergenceofmultiproteindynamicstructuresbyprinciplesofselforganizationthroughtheuseof3dspiamultiagentbasedsoftware |
_version_ |
1725202073071386624 |