| Mechanisms and free energies of enzymatic reactions J Gao, S Ma, DT Major, K Nam, J Pu, DG Truhlar Chemical reviews 106 (8), 3188-3209, 2006 | 450 | 2006 |
| An efficient linear-scaling Ewald method for long-range electrostatic interactions in combined QM/MM calculations K Nam, J Gao, DM York Journal of Chemical Theory and Computation 1 (1), 2-13, 2005 | 309 | 2005 |
| Specific reaction parametrization of the AM1/d Hamiltonian for phosphoryl transfer reactions: H, O, and P atoms K Nam, Q Cui, J Gao, DM York Journal of Chemical Theory and Computation 3 (2), 486-504, 2007 | 170 | 2007 |
| Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme Y Qi, MC Spong, K Nam, A Banerjee, S Jiralerspong, M Karplus, ... Nature 462 (7274), 762-766, 2009 | 161 | 2009 |
| A combined QM/MM approach to protein− ligand interactions: polarization effects of the HIV-1 protease on selected high affinity inhibitors C Hensen, JC Hermann, K Nam, S Ma, J Gao, HD Höltje Journal of medicinal chemistry 47 (27), 6673-6680, 2004 | 141 | 2004 |
| Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis K Nam, J Gao, DM York Journal of the American Chemical Society 130 (14), 4680-4691, 2008 | 102 | 2008 |
| Dynamics of an enzymatic substitution reaction in haloalkane dehalogenase K Nam, X Prat-Resina, M Garcia-Viloca, LS Devi-Kesavan, J Gao Journal of the American Chemical Society 126 (5), 1369-1376, 2004 | 82 | 2004 |
| Unsuspected pathway of the allosteric transition in hemoglobin S Fischer, KW Olsen, K Nam, M Karplus Proceedings of the National Academy of Sciences 108 (14), 5608-5613, 2011 | 76 | 2011 |
| Transition state stabilization and α-amino carbon acidity in alanine racemase DT Major, K Nam, J Gao Journal of the American Chemical Society 128 (25), 8114-8115, 2006 | 71 | 2006 |
| Enforced presentation of an extrahelical guanine to the lesion recognition pocket of human 8-oxoguanine glycosylase, hOGG1 CM Crenshaw, K Nam, K Oo, PS Kutchukian, BR Bowman, M Karplus, ... Journal of Biological Chemistry 287 (30), 24916-24928, 2012 | 67 | 2012 |
| Machine-learning-assisted free energy simulation of solution-phase and enzyme reactions X Pan, J Yang, R Van, E Epifanovsky, J Ho, J Huang, J Pu, Y Mei, K Nam, ... Journal of chemical theory and computation 17 (9), 5745-5758, 2021 | 65 | 2021 |
| Trapping the ATP binding state leads to a detailed understanding of the F1-ATPase mechanism K Nam, J Pu, M Karplus Proceedings of the National Academy of Sciences 111 (50), 17851-17856, 2014 | 62 | 2014 |
| The spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase β MC Koag, K Nam, S Lee Nucleic acids research 42 (17), 11233-11245, 2014 | 60 | 2014 |
| Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM Y Qi, MC Spong, K Nam, M Karplus, GL Verdine Journal of biological chemistry 285 (2), 1468-1478, 2010 | 57 | 2010 |
| Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases K Nam, J Gao, DM York Rna 14 (8), 1501-1507, 2008 | 55 | 2008 |
| Thermodynamic stability of mercury (II) complexes formed with environmentally relevant low-molecular-mass thiols studied by competing ligand exchange and density functional theory V Liem-Nguyen, U Skyllberg, K Nam, E Björn Environmental Chemistry 14 (4), 243-253, 2017 | 48 | 2017 |
| Rapid convergence of energy and free energy profiles with quantum mechanical size in quantum mechanical–molecular mechanical simulations of proton transfer in DNA S Das, K Nam, DT Major Journal of chemical theory and computation 14 (3), 1695-1705, 2018 | 45 | 2018 |
| Solvent and protein effects on the vibrational frequency shift and energy relaxation of the azide ligand in carbonic anhydrase M Garcia-Viloca, K Nam, C Alhambra, J Gao The Journal of Physical Chemistry B 108 (35), 13501-13512, 2004 | 42 | 2004 |
| Strandwise translocation of a DNA glycosylase on undamaged DNA Y Qi, K Nam, MC Spong, A Banerjee, RJ Sung, M Zhang, M Karplus, ... Proceedings of the National Academy of Sciences 109 (4), 1086-1091, 2012 | 38 | 2012 |
| Catalytic hydrogen atom transfer from hydrosilanes to vinylarenes for hydrosilylation and polymerization P Asgari, Y Hua, A Bokka, C Thiamsiri, W Prasitwatcharakorn, A Karedath, ... Nature catalysis 2 (2), 164-173, 2019 | 36 | 2019 |
