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, including the CHARMM36 and classical Drude polarizable force fields, development of novel solute and conformational sampling methodologies, understanding the physical forces driving the structure and dynamics of proteins, nucleic acids and carbohydrates and computer-aided drug design (CADD) studies including development of novel methods such as the Site Identification by Ligand Compepetive Saturation approach. A number of recent publications in these areas are highlighted below.
Research Highlight: Solution X-ray scattering scattering spectra of the DNA duplex 1DCV shown below were calculated via MD simulations in the presence of different counterions using the polarizable Drude-2013 force field [DOI]. Results show that different ion leads to changes in the scattering spectra, results that are not observed in the additive CHARMM36 force field, representing a, as yet untested, prediction by the polarizable force field. See: Savelyev and MacKerell (2015) "Differential Impact of the Monovalent Ions Li+, Na+, K+ and Rb+ on DNA Conformational Properties," Journal of Physical Chemistry Letters, 6: 212-216, 2015, [DOI],
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