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Re: [modeller_usage] How to choose the best model?

Hello!
For my protein of interest, I generate 20 models with Modeller, use Modeller's internal objective value to select the five best models, and I evaluate the models with Procheck, Whatif, Vadar, Errat and Prosa2003. I have not yet finalized my selection criteria after evaluation, but I've checked that the selected models are all of satisfactory quality according to these programs. These also help to pinpoint which areas of my multiple alignment might be problematic. 

-Charlotte Habegger-Polomat



นายจิตระยุทธ์ จิตอ่อนน้อม wrote:



Dear Modeller users
For my research the parameter which i should consider for the best model is from the evaluated program such as PROSA PROCHECK or Verify3D. For Procheck , i use the model which give a quaility of model within >80% core regions. That i used in my project so if any recomments for my research please contact me. 

Thank
Mr. JItrayut Jitonnom  CSML
Chiang Mai University
Thailand

-----Original Message-----
From: carromeu AT usp.br
Sent: Fri, 02 Dec 2005 21:41:42 -0200
To: modeller_usage@listsrv.ucsf.edu
Subject: [modeller_usage] How to choose the best model?


 Dear Modeller users,

 I'm generating diverses models to my protein (400 - is this to great?).
However I don't know how is the best parameter to look when choosing the best 
model. Objective function from Modeller, ProCheck parameters, Energy
parameters... What parameters you use and why? If using Ramachandran plot as a discriminative parameter, how great must be the parameters calculated (for 
example: >90% in favored regions,
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