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Number of overlapping pairs of atoms resulting from overlaying b12 on α1-folded gp120. The raw data were smoothed using a triangular average method with a sampling window size of 0.5 ns. The vertical line indicates where the TMD forces are lifted and equilibration is started. The small arrow at n=6 overlaps shows the number of overlaps generated when using gp120 extracted the CD4-bound crystal structure (PDB 1GC1).
