Hi all, I am looking for protein global structural superposition software which can superpose multiple proteins pairwise(more than 50), having multiple chains(more than 4)with good accuracy and speed. Also, if you can please suggest me some papers for structural alignment of proteins.
I typically use UCSF Chimera for this. You’ll probably need to do it programmatically though, as the GUI will choke on that many proteins open at once.
I have a script here which has some relevant code, but you’ll need to deconstruct it.
Check out MATT: http://cb.csail.mit.edu/cb/matt/
It does multiple alignment mainly, but can be also used for pairwise alignment. However, from your question I'm getting the sense that you're trying to superimpose all proteins at once - so it may be best suited for your needs.