Re: [modeller_usage] DOPE score based model selection

> Sorry to intrude
>
> Dear Mouses,
> May I ask what method do you use to select the best (or bests) models if
> you do not relay on DOPE score?.
>
> My experience is that DOPE, like any other score for any other
> "bioinformatics" prediction method is not perfect, but it has always
> given me good structures, perhaps not the best, but more than good
> enough (except when there are "knots" in the structure, but for that I
> have eyes :) ).
>
> thank you in advance
>
> Oscar C.S.
>
>
> Oscar Conchillo Solé
> Group of Computational Biology and Proteomics
> IBB Data Center Manager and Linux Sysadmin
> Institut de Biotecnologia I Biomedicina (UAB)
> mail: 
> telf: 0034 93581 4431; 0034 93586 8939
>
>
> On 04/16/2015 03:29 PM, Mouses Stamboulian 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:
>> <>
>> on behalf of <>
>> Sent: Thursday, April 16, 2015 4:31 PM
>> To: 
>> 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
>> _______________________________________________
>> modeller_usage mailing list
>> 
>> https://salilab.org/mailman/listinfo/modeller_usage
>> _______________________________________________
>> modeller_usage mailing list
>> 
>> https://salilab.org/mailman/listinfo/modeller_usage
>>
> _______________________________________________
> modeller_usage mailing list
> 
> https://salilab.org/mailman/listinfo/modeller_usage
>
Dear Oscar,
           I too found knots in loop-refined models which had best DOPE
scores. So is it ok to select a model with intermediate DOPE
score over the one which has lowest (best) DOPE score?
 Thanks,
  Vipul