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