4 ms·

I wonder if it would somehow be possible to use this with the protein folding game Foldit. http://fold.it/portal/ http://fold.it/portal/ Some puzzles start off

• epistasis 13y ago
  These particular algorithms are commonly used with proteins' amino acid sequences for general database searches. But since the database of protein sequences is far far smaller than typical DNA search problems, there are more sophisticated and computationally expensive algorithms such as Pair HMMs [1] or Profile HMMs [2] can be used, and for fine tuning of 3D model threading they would be a much better option, since the problem is so small. [1] http://ai.stanford.edu/~serafim/CS262_2008/notes/lecture8.pdf http://ai.stanford.edu/~serafim/CS262_2008/notes/lecture8.pd... [2] http://www.biology.wustl.edu/gcg/hmmanalysis.html http://www.biology.wustl.edu/gcg/hmmanalysis.html
• kevinwuhoo 13y ago
  Structural alignment algorithms are (generally) much different and is a much more difficult problem. The "most popular" (at least in my experience) methods are combinatorial extension [1] and DALI [2]. But I'm sure it could be done, no doubt about it. However, most people, probably besides ones at the PDB, usually don't do massive structural alignment tasks. The effort to develop and maintain such a device probably isn't feasible. [1]: http://peds.oxfordjournals.org/content/11/9/739 http://peds.oxfordjournals.org/content/11/9/739 [2]: http://www.sciencemag.org/content/273/5275/595 http://www.sciencemag.org/content/273/5275/595