Research in the MacKerell lab involves the development and application of computational methods to investigate the relationships of structure and dynamics to function in a range of biological and chemical systems. These efforts range from empirical force field development, implementation of novel sampling methodologies, understanding the physical forces driving the structure and dynamics of proteins, nucleic acids and carbohydrates and computer-aided drug design (CADD) studies. More information may be obtained on the Research page and from our list of publications. In addition, force fields and other utilities developed in the lab may be accessed via the CHARMM page.

Research Highlight: Interactions of Ser87 (purple) and Gln237 (gold) of the cytosine-5-methyltransferase from HhaI (M.HhaI) with the target cytosine base (red) and the orphan guanine base (green) during the initial stages of flipping of the target cytosine out of the DNA duplex and into that active site of M.HhaI. Left image shows the competition of Ser87 for the normal Watson-Crick base pair hydrogen bonds and the right image shows the stabilization of an early flipped state by Ser87 and Gln237. See: Huang, N., Banavali, N.K., and MacKerell, Jr., A.D. (2003) "Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase," Proceedings of the National Academy of Sciences, USA 100: 68-73.

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