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We decided to test a few protocols to locate the 1 that could best lessen RMSD from the first PDB whilst maximizing sequence recovery. All calculations are averages in excess of 50 operates from the fifty one scaffold set. All RMSDs are to native C-alpha. It is additionally doable to go through in electron density for a PDB and use that for a constraint in the course of relax (described below), but electron density will not be uniformly readily available, and we had been seeking a protocol that may operate in each and every situation regardless of whether the electron density was missing.
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