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Journal of Chemical Theory and Computation|October 5, 2021
Global Optimization of the Lennard-Jones Parameters for the Drude Polarizable Force FieldChetan R Rupakheti, Alexander D MacKerell, Benoît RouxThe Journal of Physical Chemistry. B|September 18, 2010
CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanosesE Prabhu Raman, Olgun Guvench, Alexander D MacKerellJournal of Computational Chemistry|June 9, 2004
Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulationsAlexander D Mackerell, Michael Feig, Charles L BrooksJournal of Chemical Information and Modeling|December 27, 2024
Detection of Putative Ligand Dissociation Pathways in Proteins Using Site-Identification by Ligand Competitive SaturationWenbo Yu, David J Weber, Alexander D MacKerellThe Journal of Physical Chemistry. B|June 15, 2006
Conserved patterns in backbone torsional changes allow for single base flipping from duplex DNA with minimal distortion of the double helixNilesh K Banavali, Niu Huang, Alexander D MacKerellBiophysical Chemistry|September 10, 2013
Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structureElizabeth J Denning, D Thirumalai, Alexander D MacKerellJournal of Chemical Theory and Computation|December 19, 2018
Cation-π Interactions between Methylated Ammonium Groups and Tryptophan in the CHARMM36 Additive Force FieldHanif M Khan, Alexander D MacKerell, Nathalie ReuterCarbohydrate Research|February 10, 2018
Proper balance of solvent-solute and solute-solute interactions in the treatment of the diffusion of glucose using the Drude polarizable force fieldMingjun Yang, Asaminew H Aytenfisu, Alexander D MacKerellNature Chemical Biology|June 27, 2025
Harnessing computational technologies to facilitate antibody-drug conjugate developmentAnastasia Croitoru, Asuka A Orr, Alexander D MacKerellThe Journal of Chemical Physics|December 12, 2024
Grand canonical Monte Carlo and deep learning assisted enhanced sampling to characterize the distribution of Mg2+ and influence of the Drude polarizable force field on the stability of folded states of the twister ribozymePrabin Baral, Mert Y Sengul, Alexander D MacKerellPageof 49