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Question: Structural alignment of proteins
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gravatar for shreya10nema
19 months ago by
shreya10nema • 0
shreya10nema • 0 wrote:

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.
alignment • 363 views
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modified 19 months ago by Barış Ekim • 10 • written 19 months ago by shreya10nema • 0
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gravatar for Joe
19 months ago by
Joe ♦ 18k
United Kingdom
Joe ♦ 18k wrote:

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.

https://github.com/jrjhealey/bioinfo-tools/blob/master/strucfit.py#L184
ADD COMMENT • link written 19 months ago by Joe ♦ 18k
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gravatar for Barış Ekim
19 months ago by
Barış Ekim • 10
Cambridge, MA, USA
Barış Ekim • 10 wrote:

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.
ADD COMMENT • link written 19 months ago by Barış Ekim • 10
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