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