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PostPosted: Thu Oct 09, 2014 8:22 am 
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Joined: Thu Oct 09, 2014 8:05 am
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I am trying to test a hypothesis to be validated in vitro. I am working with a protein that has been known to evade immune responses. Its crystal structure has been solved, so I obtained field isolate samples and modelled all 21 sequences by homology. I have a hypothesis that the polymorphisms within these sequences may result in structural differences that result in immune evasion. I therefore, used the command :arrow: "align mobile, target, cycles=0" in Pymol and one of the results was RMS = 3.412 (601 to 601 atoms). My cutoff for structural similarity is 3 angstroms, so for example, in the above case I would conclude difference in structures.

I am justified in my methodology????


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