Re: [modeller_usage] DOPE score based model selection

[Oscar Conchillo Solé <>]

Dear Vipul,
Totally ok! knots are artificial and you should totally ignore those 
models with them (once I had to visualize almost 400 models until I 
found one without them)

And answering your original question:
If I don't remember wrong, automodel also includes the function 
loopmodel for those regions that align with nothing (gaps) so if you are 
generating enough models in your first run, probably you do not need 
loopmodel.

cheers
OCS


https://salilab.org/modeller/FAQ.html#14

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 09:09 PM,  wrote:
> > 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
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> >      
> 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
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