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
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
Hi,
I hope this helps: http://salilab.org/publications/
Thanks, Bozidar
-----Original Message----- From: owner-modeller_usage@salilab.org [mailto:owner-modeller_usage@salilab.org] On Behalf Of Luca Settimo Sent: Monday, April 15, 2002 11:41 AM To: 'Modeller Usage List' Subject: theory info
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
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Andras Fiser -
Bozidar Jerkovic -
Luca Settimo