Re: [modeller_usage] DOPE score based model selection

>Thank you all. Your suggestions were very helpful in clarifying my doubts.
    Vipul

Dear Vipul,
>
> What you are referring to is actually a whole field in the computational
> structural modeling. Its called "Model Quality Assessment". You can
> perhaps
> run something like TMScore or other methods like ProQ2 etc (downloadable
> methods) or upload them to some of the best MQAP servers. A good place to
> search for the best methods is the CASP result page (
> http://predictioncenter.org/casp11/qa_analysis.cgi).
>
> You can run your models in these methods and see if they give you an
> appropriate ranking or not. All of them will give you a score just like
> DOPE score.
>
> Cheers
>
> Arjun
>
> On Fri, Apr 17, 2015 at 1:47 PM, Oscar Conchillo Solé
> <>
> wrote:
>
>> 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
>>>>> _______________________________________________
>>>>> modeller_usage mailing list
>>>>> 
>>>>> https://salilab.org/mailman/listinfo/modeller_usage
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>>>>> 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
>>> _______________________________________________
>>> modeller_usage mailing list
>>> 
>>> https://salilab.org/mailman/listinfo/modeller_usage
>>>
>>>
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>
>
>
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> *****************************************************
> Arjun Ray
>
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