Re: [modeller_usage] How to choose the best model?
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@usp.br Sent: Fri, 02 Dec 2005 21:41:42 -0200 To: modeller_usage@salilab.org 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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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@usp.br > Sent: Fri, 02 Dec 2005 21:41:42 -0200 > To: modeller_usage@salilab.org > 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, > > > > > ---------------------------------------------------------------------------------- > > http://www.chaiyo.com ไชโยเมล์ - ฟรีอีเมล์รูปแบบใหม่ สดใสกว่าเดิม... > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > http://salilab.org/mailman/listinfo/modeller_usage >
Hello Charlotte!
Thanks for your advice! I'm working with the function value from Modeller. But, I believe that need to refine my models (I'm finding too high values). What are the ranges of values that you find with your models? I'm thinking in refine my alignment.
Thanks, Cassiano Carromeu.
Citando Charlotte Habegger-Polomat chpoloma@rsvs.ulaval.ca:
> 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 > > > > ¹Ò¨ԵÃÐÂØ·¸ì ¨ÔµÍè͹¹éÍÁ 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@usp.br > > Sent: Fri, 02 Dec 2005 21:41:42 -0200 > > To: modeller_usage@salilab.org > > 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, > > > > > > > > > > > ---------------------------------------------------------------------------------- > > > > > http://www.chaiyo.com äªâÂàÁÅì - ¿ÃÕÍÕàÁÅìÃٻẺãËÁè Ê´ãÊ¡ÇèÒà´ÔÁ... > > _______________________________________________ > > modeller_usage mailing list > > modeller_usage@salilab.org > > http://salilab.org/mailman/listinfo/modeller_usage > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > http://salilab.org/mailman/listinfo/modeller_usage >
participants (3)
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carromeu＠usp.br -
Charlotte Habegger-Polomat -
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