 The processes of protein folding and binding can be simulated using such technique as molecular mechanics , in particular , molecular dynamics and Monte Carlo , which increasingly take advantage of parallel and distributed computing ( Folding @ home project ; molecular modeling on GPU ) . The folding of small α @-@ helical protein domains such as the villin headpiece and the HIV accessory protein have been successfully simulated in silico , and hybrid methods that combine standard molecular dynamics with quantum mechanics calculations have allowed exploration of the electronic states of rhodopsins . 
 The processes of protein folding and binding can be simulated using such technique as molecular mechanics , in particular , molecular dynamics and Monte Carlo , which increasingly take advantage of parallel and distributed computing ( Folding @ home project ; molecular modeling on GPU ) . The folding of small α @-@ helical protein domains such as the villin headpiece and the HIV accessory protein <a href='been_done' title='1'><mark>have</mark></a> been successfully simulated in silico , and hybrid methods <a href='null_relcl' title='2'><mark>that</mark></a>combine standard molecular dynamics with quantum mechanics calculations <a href='been_done' title='3'><mark>have</mark></a> allowed exploration of the electronic states of rhodopsins . 
The processes of protein folding and binding can be simulated using such technique as molecular mechanics , in particular , molecular dynamics and Monte Carlo , which increasingly take advantage of parallel and distributed computing ( Folding @ home project ; molecular modeling on GPU ) . The folding of small α @-@ helical protein domains such as da villin headpiece and the HIV accessory protein done been successfully simulated in silico , and hybrid methods combine standard molecular dynamics with quantum mechanics calculations done allowed exploration of the electronic states of rhodopsins .