Wenbo Yu, Kenno Vanommeslaeghe, Fengtian Xue, MacKerell Jr., A.D., Guvench, O., "Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma," JCI The Journal of Clinical Investigation, Volume 126, Issue 9, Pages 3159-3626. [DOI]

Alexander D. MacKerell Jr., Raphael Simon, Mingjun Yang, "Cover photograph with molecular model showing three repeats of Salmonella enterica serovar Typhimurium O-polysaccharide (OPS) (O:1,4,12) and glucosylation at the central OPS unit," CVI Clinical and Vaccine Immunology, December 2016, Volume 23, Issue 12 [DOI]


Wenbo Yu, Kenno Vanommeslaeghe, Fengtian Xue, Alexander D. MacKerell Jr., "Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations," Journal of Chemical Theory and Computation, 10: 2281-2290, 2014. [DOI]

Huang, J., Lopes, P.E.M., Roux, B., and MacKerell, A.D., Jr., "Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model," Journal of Physical Chemistry Letters, 5: 3144-3150, 2014. [DOI]


Shim, J., Zhu, X., Best, R.B., and MacKerell Jr., A.D. "(Ala)4-X-(Ala)4 as a model system for the optimization of the χ1 and χ2 amino acid side chain dihedral empirical force field parameters." Journal of Computational Chemistry, 34: 593-603, 2013. [DOI]

Nagagarajan, S., Xue, F., and MacKerell, A.D., Jr. “Impact of substrate protonation and tautomerization states on interactions with the active site of Arginase I,” Journal of Chemical Information and Modeling, 53: 452–460, 2013. [DOI]


Foster, T.J., MacKerell Jr., A.D. and Guvench, O. "Balancing Target Flexibility and Target Denaturation in Computational Fragment-Based Inhibitor Discovery," Journal of Computational Chemistry, 33:1880-91, 2012. [DOI]


Raman, E.P. Yu, W. Guvench, O. and MacKerell, Jr. A.D. "Reproducing Crystal Binding Modes of Ligand Functional Groups using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations," Journal of Chemical Information and Modeling 51: 877-896, 2011. [DOI]


Baker, C. Lopes, P. Zhu, X. and MacKerell, Jr. A.D. "Accurate Calculation of Hydration Free Energies using the CHARMM Drude Polarizable Force Field," Journal of Chemical Theory and Computation 6: 1181-1198, 2010. [DOI]


Zhong, S. and MacKerell, Jr. A.D. "Binding Response: A Descriptor for Selecting Ligand Binding Site on Protein Surfaces," Journal of Chemical Information and Modeling 47: 2303-2315, 2007. [DOI]