Volume 4, Number 2, p. 50-63
HSIM: a simulation programme to study large assemblies of proteins
Patrick Amar 1,2, Gilles Bernot 2, and Victor Norris 3
1
Laboratoire de Recherches en Informatique, Université Paris Sud & CNRS UMR 8623, 15 avenue George Clémenceau, F-91405 Orsay CEDEX
2
La.M.I. Université d¹Evry Val d¹Essonne & CNRS UMR 8042, Tour Evry 2, 523 Place des terrasses de l¹agora, F-91000 Evry
3
Laboratoire des Processus Intégratifs Cellulaires, CNRS UMR 6037, Faculté des Sciences et Techniques, Université de Rouen, F-76821 Mont-Saint-Aignan CEDEX
To study the assembly, the movements and the dissociation of large numbers of molecules in a virtual cell, a simulation program, HSIM, has been developed. The simulator is driven using a description of the model system written in a language we have also developed that does not limit the simulation program to a particular model. We present here the simulation of two completely different models: the growth of actin-like filaments in a prokaryotic cell, and the association of proteins into large assemblies and their dissociation.
Keywords: hyperstructures, modelling, protein-protein interactions, simulation, virtual cell