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: txino@bioinf.uab.es
telf: 0034 93581 4431; 0034 93586 8939

On 04/16/2015 09:09 PM, vipul@nccs.res.in 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: txino@bioinf.uab.es
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:
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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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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