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To facilitate the computational study of proteins in the AlkB family and related α-ketoglutarate/Fe(II)-dependent dioxygenases, Xueqin Pang, Keli Han, and Qiang Cui on page 1620 test a simple modeling strategy for the non-heme Fe(II) site in which the iron is represented by a simple +2 point charge with Lennard–Jones parameters. Molecular dynamics simulations indicate that the crystal structure of AlkB-dsDNA undergoes significant structural relaxations in a solution. This explains why, unlike another member of the AlkB family also studied here, AlkB prefers ssDNA over dsDNA as the natural substrate for DNA repair.