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Abstracted Protein Simulator

The Abstracted Protein Simulator models proteins interacting in 3D, at a mesoscopic level. It was designed for studying the self-assembly and operation of protein machines containing 10s or 100s of proteins, and operates at a coarser temporal and spatial scale than most simulators.

Our main model system is the development of the post synaptic density, a complex assembly of ion channels and cytoskeleton which is a critical part of learning and memory in the synapse. We have also been testing the simulator on self assembly of simple viruses from their constituent proteins, since more complete molecular data sets are available for viruses than neurons.


Protein structures can be input in .pdb format from databases.

The structure can be simplified by grouping by amino acid...

...or clustered into a simpler structure.

Bonds can be defined and added to the protein template.

The simulation is run

and the self assembled structures viewed.