Am 05.10.2009, 06:13 Uhr, schrieb Afonso Duarte <
afonsomduarte@...>:
> 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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