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Protein secondary structure prediction

I'm trying to predict the protein secondary and 3-D structure for the sequence [Q1NN20] and need some help getting the ball rolling. I'm getting confused with how and when to use Jpred, swiss-mod, ...
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Visualizing secondary RNA structure binding to target

I am designing synthetic ribozymes, and need to see the secondary structure that arises from its flanking arms binding to a target mRNA. I've used Mfold as well as IDT's OligoAnalyzer (Hairpin), but ...