Greetings!
I am Bennett Henzeler, working as a Research Intern in the area of HIV infection at ICMR-NIRT, India. Recently we used QUARK and I-Tasser Modeller for prediction of highly similar sequences (Aligned them and verified using MEGA and CLUSTAL W). But the models predicted were totally different (we tried to superimpose them using pymol and the RMSD was 17). We have 44 such similar sequences, out of which 5 were done with QUARK and I-Tasser. The difference in the models has put a pause on our work. We were planning to predict the function of the protein based on these structures.
The secondary structures predicted by both the program are same but the tertiary structures vary. So we have a doubt whether the folding may differ from one to another even with sequence high homology and similar secondary structures. The below file attached m1asp1ref is I-Tasser and m1asp1 is Quark
For further assistance all the sequences uploaded from mail id's ending with nirt.res.in are from our project centre, you can look into those structures predicted
Regards
Bennett Henzeler
benz4166henzeler@gmail.com
C/o Ashokkumar Manickam
ICMR-NIRT