A convenient simulation environment
for protein folding
as well as other polymer dynamics studies. It is similar in principle to the Ising model
used in physics to study ferromagnetism
Consists primarily of 2-D or 3-D lattice with a simplified chain of residues moving across it according to various rules. This can look surprisingly like a game of GO, with black and white circles on a grid. However, the intention is that the chain of residues should move from an unfolded state to a folded or native state.
Depending on the shape of the underlying lattice, the moves can be quite rigid, simple ones (for a square lattice) or more realistic, fluid moves (for hexagonal lattices). Of course, square lattices (grids) are much easier to program than hexagonal ones!
As the positions of the residues are updated on the model, each one has to be checked for interactions with the others. An interaction between two residues can be whatever you feel like, but usually there are two types (coloured black and white, like the Go pieces) with one representing hydrophobic residues and one hydrophilic residues. A table of interaction energies is necessary (white-black, black-black and white-white) and these are summed across the whole protein to get the 'energy' of a particular state.