To generate a model for my target protein I have been using a number of prediction tools. However, Phyre2 and I-TASSER servers do not provide me with the correct models. The sequence of my target protein was obtained in the FASTA format and the sequence was copied and pasted into all the servers used.
For Phyre2 I used the intensive mode. The template structure predicted 5 alpha-helices and 4 beta-strands, however the model only presented 2 alpha-helices and 3 beta-strands. When looking at the template all the alpha-helices have a high confidence score of 9 out of 9, where 9 is the highest confidence score. Similarly the beta-strands had also a high confidence score of 7 out of 9. Also the disorder confidence was low for each of the structures.
For I-TASSER the secondary structure template predicted 5 alpha-helices and 4 beta-sheets. From the top 5 final models predicted by I-TASSER model 1 with the highest C-score of -4.05 was used. The model represented 6 alpha-helices and no beta-strands were modelled. The template presents high confidence score for each structure similarly to Phyre2 server. What could be the problem for the models to not correlate to the template? Thank you in advance for your help.
Most likely, the accents for the task are incorrectly placed. The underlying problem or cause is misformed
Kindly try to make a multiple sequence alignment for your target and the templates used by the Phyre2 and I-TASSER to see the conserved regions. I think the reason is either low sequence identity or your target seq has no solved homolog structure at all.
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