RosettaDesign: Pack Rotamers

The following movie shows the amino acid substitutions tried during a RosettaDesign simulation. RosettaDesign uses randomly chosen rotamers, simulated annealing and a monte carlo acceptance criteria to identify low energy sequences compatible with a starting structure. This movie shows every accepted substitution and the color of the protein changes from white to dark green as an indication of the 'temperature' of the simulated annealing protocol. Feel free to download this movie and use it in your teaching or presentations.

Rosetta Folding

The following movie shows the trajectory of a single Rosetta folding simulation. Millions of similar simulations are performed as part of a Rosetta structure prediction experiment. The simulation begins with a completely extended chain, and proceeds through several stages that try to fold the sequence using a 'move set', a monte carlo acceptance criteria, and energy functions that favor burial of hydrophobic residues. Central to the Rosetta 'move set' is the insertion of 3-residue and 9-residue fragments selected from high-resolution protein crystal structures, these moves are obvious in the early stages of the folding protocol. Feel free to download this movie and use it in your teaching or presentations.