The biggest qualm I have is that it's almost impossible to restore proper alignment to a twisted beta sheet. For example in the beta barrel puzzle, sidechains which should be on the interior get stuck on the outside because you can't force them through the neighboring sheet (the beta sheet gets twisted in sideways). I think two tools could fix that: A backbone torque or the option to rotate a sidechain without feeling the stuff you want to move it through.

If every move the user can make uses the MD potential I don't see how people can help relieve local minima by taking steps that dynamics on the MD potential wouldn't! You should be able to shut the potential off!.

Great Scientific game though and good work

John Parkhill
Head-Gordon Group
University of California, Berkeley.