Results - 2012
The SIMONA Framework
SIMONA is an abbreviation for "simulation of molecular and nanoscale systems". This framework has grown out of our POEM project, and is the backbone for our current POEM@HOME applications.
SIMONA implements Monte Carlo based methods for stochastic simulations. Our application area includes protein conformational changes, protein-protein association, small molecule protein docking and the growth of nanoscale clusters of organic molecules.
We used POEM@HOME to study the dimerization of the fire ant venom allergen (2YGU), which occurs as a homodimer in its native state, stabilized via a disulfide bond.
With our simulations we were able to find the native conformation as a free energy minimum in absence of a potential modeling the disulfide bridge.
Further information is available in the article SIMONA 1.0: an efficient and versatile framework for stochastic simulations of molecular and nanoscale systems, published in the Journal of Computational Chemistry. The software is free for academical use, and can be downloaded here.