IUBio

Free software to display protein secondary structure in 3D view?

Simon Andrews simon.andrews at bbsrc.ac.uk
Tue Mar 9 08:13:37 EST 2004


bigc wrote:

> Hi Gurus,
> 
> I'm a newbee to bioinfomatics. It seems that via the secondary
> structure we can roughly predict the protein's 3D structure. 

Err no.  Not really.  There are usually many different folds which have 
the same linear secondary structure organisation.

The closest you can get to what you describe is doing Fold Fitting (or 
threading).  This uses secondary structure and threading information to 
predict a fold for a sequence which may have no obvious homologs which 
have had their structures solved.

Take a look at:

http://www.sbg.bio.ic.ac.uk/~3dpssm/

http://123d.ncifcrf.gov/123D+.html

http://ffas.ljcrf.edu/ffas-cgi/cgi/ffas.pl

Hope this helps

Simon.



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