qPCR will be done with SybrGreen
Pubmed or Google Scholar will help you find publications that have done real time for your target. Otherwise IDT and Roche have great resources for primer design:
http://www.idtdna.com/pages/scitools
https://lifescience.roche.com/webapp/wcs/stores/servlet/CategoryDisplay?tab=Assay+Design+Center&identifier=Universal+Probe+Library&langId=-1
How to calculate the RMSD values for a MD simulation using MOE?
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