>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 > txino@bioinf.uab.es > 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: 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.orgmodeller_usage-bounces@salilab.org >>>>> on behalf of vipul@nccs.res.invipul@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 >>>>> _______________________________________________ >>>>> modeller_usage mailing list >>>>> modeller_usage@salilab.org >>>>> https://salilab.org/mailman/listinfo/modeller_usage >>>>> _______________________________________________ >>>>> modeller_usage mailing list >>>>> modeller_usage@salilab.org >>>>> https://salilab.org/mailman/listinfo/modeller_usage >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> modeller_usage mailing list >>>> modeller_usage@salilab.org >>>> 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 >>> modeller_usage@salilab.org >>> https://salilab.org/mailman/listinfo/modeller_usage >>> >>> >> _______________________________________________ >> modeller_usage mailing list >> modeller_usage@salilab.org >> https://salilab.org/mailman/listinfo/modeller_usage >> > > > > -- > **************************************************** > > The dream is not that you see in sleep , dream is which does not let you > sleep. ~Dr. Abdul Kalam (Former President of Republic of India) > ***************************************************** > Arjun Ray > > Mobile : +919582948808 > Email : arjun@ebi.ac.uk / arjun@cbr.su.se arjun.ray@cbr.su.se > Lab Page: http://www.igib.res.in/ssg/index.html > Personal Page: http://www.igib.res.in/ssg/Arjun.html > *********************************************** > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >