My protein is a heterodimer of two chains produced from a single polypeptide due to post-translational proteolytic cleavage. The templates (x-ray structures) also consists of two chains. How can I input sequence as two chains? I use iTasser. It is important because after cleavage into two chains their is a conformational change in the loop.
Is the cleave site of your protein same with the template model? if you provide more details, I can able to help you @ Khawar Sohail Siddiqui
Yes its identical. I have been suggested to use TACOS and SPRING (iTASSER) which can take chains A and B input separately.
Yes its identical. Some one suggested to use TACOS and SPRING (iTASSER) which can take chains A and B input separately.
Thanks a lot
Khawar Sohail Siddiqui what is the sequence similarity between your structure and the template?
It would be better to model each chain separately and then superimpose your models with the template to fix the relative orientation of chains.
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