Google Groups no longer supports new Usenet posts or subscriptions. Historical content remains viewable.
Dismiss

How to compare multiple pdb's according to secondary struc+torsion angles

0 views
Skip to first unread message

Afonso Duarte

unread,
Oct 5, 2009, 6:13:13 AM10/5/09
to prot...@magpie.bio.indiana.edu
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 ?

Thanks in advance


Afonso

Dr Engelbert Buxbaum

unread,
Oct 7, 2009, 9:25:58 AM10/7/09
to

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.

0 new messages