Structural alignment algorithms are (generally) much different and is a much more difficult problem. The "most popular" (at least in my experience) methods are

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