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Journal of the American Chemical Society|January 28, 2015
Spatial analysis and quantification of the thermodynamic driving forces in protein-ligand binding: binding site variabilityE Prabhu Raman, Alexander D MacKerellPhysical Chemistry Chemical Physics : PCCP|June 27, 2020
Transition between [R]- and [S]-stereoisomers without bond breakingShampa Raghunathan, Komal Yadav, V C Rojisha, et al.Journal of Chemical Theory and Computation|January 23, 2018
Polarizable Empirical Force Field for Halogen-Containing Compounds Based on the Classical Drude OscillatorFang-Yu Lin, Alexander D MacKerellPlos One|May 14, 2009
Characterizing structural transitions using localized free energy landscape analysisNilesh K Banavali, Alexander D MackerellJournal of Molecular Biology|June 8, 2002
Free energy and structural pathways of base flipping in a DNA GCGC containing sequenceNilesh K Banavali, Alexander D MacKerellJournal of the American Chemical Society|January 17, 2012
Intrinsic contribution of the 2'-hydroxyl to RNA conformational heterogeneityElizabeth J Denning, Alexander D MacKerellJournal of Computational Chemistry|September 14, 2019
Improved Modeling of Cation-π and Anion-Ring Interactions Using the Drude Polarizable Empirical Force Field for ProteinsFang-Yu Lin, Alexander D MacKerellACS Omega|June 12, 2023
Influence of Mg2+ Distribution on the Stability of Folded States of the Twister Ribozyme Revealed Using Grand Canonical Monte Carlo and Generative Deep Learning Enhanced SamplingMert Y Sengul, Alexander D MacKerellJournal of the American Chemical Society|March 6, 2003
2D conformationally sampled pharmacophore: a ligand-based pharmacophore to differentiate delta opioid agonists from antagonistsDenzil Bernard, Andrew Coop, Alexander D MacKerellJournal of Medicinal Chemistry|March 21, 2007
Quantitative conformationally sampled pharmacophore for delta opioid ligands: reevaluation of hydrophobic moieties essential for biological activityDenzil Bernard, Andrew Coop, Alexander D MacKerellPageof 49