[Protein-analysis] Re: How to compare multiple pdb's according to secondary struc+torsion angles

Dr Engelbert Buxbaum via proteins%40net.bio.net (by engelbert_buxbaum from hotmail.com)
Wed Oct 7 08:25:58 EST 2009


Am 05.10.2009, 06:13 Uhr, schrieb Afonso Duarte <afonsomduarte from gmail.com>:

> Dear All,
>
> I have approximately 40 to 50 pdb structures of homologous proteins
> that I want to compare.
> I am interested on plotting the sequence vs (secondary
> structure/torsion_angles/accessibility/hydrophobicity). I have tried
> software like VMD and WHATIF to do such plots (or part of them) but I
> am getting problems when the number of structures compared is getting
> close to 10...
> Does anybody knows a software/script/webpage that allows such
> comparison of such number of pdb ?

DeepView (formerly the Swiss PDB viewer, www.expasy.ch/spdbv/) can  
superimpose structures for optical comparison. It can also save a list of  
phi/psi values (Save - Ramachandran plot) for each protein as text file.  
You could then enter these values into a spreadsheet for further analysis,  
or write your own software to do further evaluation. It may be necessary  
to align the proteins first with Clustal, so that you compare like with  
like.


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