The best way is a continous large scale evaluation of automated programs, as it is implemented e.g in EVA http://pipe.rockefeller.edu/~eva/
Modeller is not yet included in this evaluation but hopefully will be soon.
Andras
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