text: user1842: Are there any algorithms already in existence for reverse protein folding/docking (e.g. taking a desired surface map/docking profile and generating DNA which will produce a protein to fold into it?)
  Protein folding seems straightforward (though computationally intensive) and protein docking is likewise straightforward, but thus far I haven't come across any protein unfolding algorithms, though I might just be searching for the wrong keywords.
  Any advice in this area?
  
  user73: The researchers behind FoldIt have the occasional design challenges that use human game players to help design proteins to fit a structure. 
  However, even with a known protein sequence there's still a lot of labwork involved in trying to find a good working DNA sequence. Just generating the DNA sequence is a difficult task due to redundancy in the genetic code (i.e. 64 codons for 20 amino acids + stop signals). When that is combined with cell-specific tRNA frequencies that can influence the timing of amino acid incorporation (and therefore how a protein folds as it is created), creating a sequence that reliably fits a shape ends up being quite difficult.
  
original_text: 1842: <p>Are there any algorithms already in existence for reverse protein folding/docking (e.g. taking a desired surface map/docking profile and generating DNA which will produce a protein to fold into it?)</p>
  
  <p>Protein folding seems straightforward (though computationally intensive) and protein docking is likewise straightforward, but thus far I haven't come across any protein unfolding algorithms, though I might just be searching for the wrong keywords.</p>
  
  <p>Any advice in this area?</p>
   73: <p>The researchers behind <a href="http://fold.it/portal/blog" rel="nofollow noreferrer">FoldIt</a> have the occasional <em>design challenges</em> that use human game players to help design proteins to fit a structure. </p>
  
  <p>However, even with a known protein sequence there's still a lot of labwork involved in trying to find a good working DNA sequence. Just generating the DNA sequence is a difficult task due to redundancy in the genetic code (i.e. 64 codons for 20 amino acids + stop signals). When that is combined with cell-specific tRNA frequencies that can influence the timing of amino acid incorporation (and therefore how a protein folds as it is created), creating a sequence that reliably fits a shape ends up being quite difficult.</p>
  