From: Min-yi Shen <minyishen@gmail.com>
Sent: Thursday, April 16, 2015 4:57 PM
To: Mouses Stamboulian
Cc: vipul@nccs.res.in; modeller_usage@salilab.org
Subject: Re: [modeller_usage] DOPE score based model selection

Dope has the tendency to pick the most compactly packed model because it favors contacts. For disordered regions of proteins this may or may not be a good thing. 

On Thursday, April 16, 2015, Mouses Stamboulian <mouses.stamboulian@lau.edu> wrote:

the DOPE score is not a correct indication from my experience. Ive modelled proteins of already known structures, then calculated their RMSD by aligning my computed models through modeller with the structure found in PDB. it has shown that not always the model with the lowest DOPE or nomralized DOPE for that matter has the best RMSD results with the PDB structure.

________________________________________
From: modeller_usage-bounces@salilab.org <modeller_usage-bounces@salilab.org> on behalf of vipul@nccs.res.in <vipul@nccs.res.in>
Sent: Thursday, April 16, 2015 4:31 PM
To: modeller_usage@salilab.org
Subject: [modeller_usage] DOPE score based model selection

Dear Modeller_usage members,

Is it necessary to select the best protein model based on DOPE scores?
I have made 100 models of a ~260 residue protein (enzyme) using Modeller.
Then I chose the best model based on the DOPE Score and did loop
refinement on a 16-residue long loop (50 refined models created) located
at active site cleft. In loop-refined model the loop occludes the active
site cleft, but in another loop-refined model (with intermediate DOPE
score) it is alright. Can I use this loop-refined model? Also, is it
essential to refine the loop even when some initial Models have good
conformations of the loop? Any suggestions would be very helpful.

Thanks in advance,
      Vipul
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