 A primary feature of the Rosetta @ home graphical user interface ( GUI ) is a screensaver which shows a current workunit 's progress during the simulated protein folding process . In the upper @-@ left of the current screensaver , the target protein is shown adopting different shapes ( conformations ) in its search for the lowest energy structure . Depicted immediately to the right is the structure of the most recently accepted . On the upper right the lowest energy conformation of the current decoy is shown ; below that is the true , or native , structure of the protein if it has already been determined . Three graphs are included in the screensaver . Near the middle , a graph for the accepted model 's free energy is displayed , which fluctuates as the accepted model changes . A graph of the accepted model 's root mean square deviation ( RMSD ) , which measures how structurally similar the accepted model is to the native model , is shown far right . On the right of the accepted energy graph and below the RMSD graph , the results from these two functions are used to produce an energy vs. RMSD plot as the model is progressively refined . 
