Actually I am facing the problem in selecting the best model from the 10 models but In some paper it was given that the best model can be selected on the basis of dope score, whereas in Andrej sali's paper of homology modelling they have talked about objective function (best model can be selected on basis of less objective function value as well as they have talked about dope score too. while comparing both parameters I am getting different results then found RMSD vales for all the 10 models with the template and my RMSD matches the dope score results. so, please suggest me something good for selecting the best model or finding RMSD can be good for selecting the best model ?? Confused in dope score and objective function values for the same target generating 10 different model.
You may use TM-score (https://zhanglab.ccmb.med.umich.edu/TM-score/) to select the best model from the 10 models. But if the native structure is not available, then you may use dope score or any scoring (QA) methods to select the TOP1 model from the 10 models.
Hi Mohd,
The DOPE model score is designed for selecting the best structure from a collection of models built by MODELLER. The score is unnormalized with respect to the protein size and has an arbitrary scale, therefore scores from different proteins cannot be compared directly, and according to the DOPE model score definition that with the lowest DOPE score is the best model.
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