> 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