The best way is a continous large scale evaluation of automated
programs, as it is implemented e.g in EVA
Modeller is not yet included in this evaluation but hopefully will be
Luca Settimo wrote:
> Dear Modeller friends,
> I would appreciate if you could suggest me some references (literature)
> about how an homology modeling program (like Modeller) is evaluated. I
> know that the rmsd between the model and the real structure (like the
> CASP approach, just to be clear) is the most common way to study this.
> But what about the rsmd of all atoms of the proteins versus the C alpha
> atoms? and what about the side chain position in the binding site?
> Are there some studies about that?
> I have start to read literature about that, but I must confess that I
> didn´t find answers... only C alpha and threading methods...
> Do you have more informations that can help me?
> What is the article that validate Modeller (from this point of view)? is
> it Proteins (1995) 23(3) 318-26?
> Thanks in advance
> Luca Settimo
Andras Fiser, PhD # phone: (212) 327 7216
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras