When I used I-TASSER, SWISS-MODEL, modeller homology modeling for my protein sequence, the results are much different, so I don't know which is the better. Anyone can give me some advice?
largely depends on the quality of templates. I-TASSER will give a better answer if there is not a closely homologous template with a structure.
http://zhanglab.ccmb.med.umich.edu/I-TASSER/about.html
I-tasser will give you a confidence estimate for your prediction
http://zhanglab.ccmb.med.umich.edu/I-TASSER/example/cscore.txt
Modeller and swiss-model are much faster and may give a better answer if there is a very closely related template
You should check the results in Ramachandran plot and see which one gives better result.
Hello,
Different homology modelling softwares will provide you with different models. I would suggest you to compare all the models using validation and evaluation tools. There are several tools available such as PROCHECK. PROCHECK would enable you to attain Ramachandran plots. Based on the plots you can rank your models and then select the best one. Perform QMEAN score and Z score tests using QMEAN server tool. Also take into account the G-Factor as well.
Hope this helps.
Regards.
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