I have built my GPCR homology model but I want to create a disulfide bond in my extracellular loop region. Can I do this in Prime?

Yes. If the two sulfur atoms of the cysteines are in close proximity then you could simply add a bond between these two atoms, minimize and then refine the loop regions. If they are not, Prime can be used to predict a loop region, while using a distance constraint, to ensure that the newly predicted loop does place the two sulfur atoms in close proximity. The disulfide bond can then be manually added, for example with the Draw tool on the Build toolbar.

Keywords: Prime, disulphide, disulfide, GPCR, constraint, Maestro, Prime

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