Question: Structural alignment of proteins
0
gravatar for shreya10nema
19 months ago by
shreya10nema0 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
ADD COMMENTlink modified 19 months ago by Barış Ekim10 • written 19 months ago by shreya10nema0
3
gravatar for Joe
19 months ago by
Joe18k
United Kingdom
Joe18k 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 COMMENTlink written 19 months ago by Joe18k
0
gravatar for Barış Ekim
19 months ago by
Barış Ekim10
Cambridge, MA, USA
Barış Ekim10 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 COMMENTlink written 19 months ago by Barış Ekim10
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