I used MODELLER as a tool to accomplish comparative protein 3D structure prediction of my protein of interest. However I believe due to the poor alignment through the last 70 base pair, all gaps, I ended up having straight lined up structure for the last 70 aminoacids arrangement. Any suggestions what to do from this point?. Should cut the protein that results in consecutive gaps after the alignment? But it would not be realistic. I am pretty confused
If those 70 residues are found in any other protein structure you can do multi template modelling or you can try to model those residues with I-TASSER server.
https://salilab.org/modeller/tutorial/advanced.html
http://zhanglab.ccmb.med.umich.edu/I-TASSER/
Yes you can try another template of your modeller alignment on the basis of resolution value, that should be minimum in your alignment tree.
if u are unable to find ur structure then you should go for I-Tasser
You can use ModellerJ. It's an easy to use interface for
modeller. See this video https://www.youtube.com/watch?v=mBgqGpztcmM&t=63s
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