Subject: Summary of Help with Homology SWISS-MODEL

From: "Juan Alexander Padron Garcia" <[email-masked]>
Date: Mon, 18 Dec 2000 08:12:20 -0600

Dear All:

First I would like to thanks to all the people who reply to my question. All the comments has been extremely usefull. Thanks again, Merry Chrismas and Happy New Millenium.

Best Regards,
Juan Alexander Padron
Molecular Modeling Laboratories
Pharmaceutical Chemistry Center
La Havana, Cuba

SUMARY

Question:
I have obtain a homology model of a protein of unknown structure using SWISS-MODEL, but I would like to validate the method in order to see if it works OK on this type of protein family. I think that the best way will be modeling a known structure of the family and finding the rmsd of the model with the real one, but I will need to tell to the program to ignore that PDB file from the RCSB. Is there a way to do that? Is there any program that could do it? 

Answers
>From Gennady Poda:
check this out: http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html
>From Gales Rhodes
Use Deep View (SwissPdbViewer) for your homology modeling, and you will be
able to choose your templates rather than letting SwissModel choose them
for you.

For help with this, see

http://www.usm.maine.edu/spdbv/text/modeling.htm

If you are new to Deep View, see

http://www.usm.maine.edu/~rhodes/SPVTut/index.html

>From Don Gregory
Structural homology modeling has been around for quite some time,
and is regarded by many in the field, as a reliable method for
generating starting models.
Generally, the 'lower-limit' people have found, by experience, is
that of having 30% identity in the area of interest, whether it is
the whole protein, a domain, or an active site.  Of course,
evolutionary pressures tend to make the identity quite a bit higher
in active sites.
Several excellent papers on the techniques can be found on the
web-site of Professor Andrej Sali, Rockefeller University.  He
has created an automated homology program, called Modeler.
http://guitar.rockefeller.edu/publications/ref/ref.html

Another thing I could suggest, would be to find a *family* of
similar structures.  Use one as the template, and build by
homology, another family memeber who's structure is known,
and then see how 'acceptable' that is to you.
I might suggest using something like Profiles-3D to test the
validity of the build model as well.  This is a program developed
by Professor David Eisenburg at UCLA, and is quite well
respected in 'testing' a build model with respect to its likelihood
of being a reasonable structure.  You can find more info on this
at:
http://www.doe-mbi.ucla.edu/people/fischer/BENCH/benchmark1.html