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Kwangho Nam, Ph.D. - Publications

Affiliations: 
2006 University of Minnesota, Twin Cities, Minneapolis, MN 
Area:
Physical Chemistry
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29 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Shigdel UK, Ovchinnikov V, Lee SJ, Shih JA, Karplus M, Nam K, Verdine GL. The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase. Nature Communications. 11: 4437. PMID 32895378 DOI: 10.1038/S41467-020-18290-2  0.304
2020 Li Y, Nam K. Repulsive soft-core potentials for efficient alchemical free energy calculations. Journal of Chemical Theory and Computation. PMID 32559374 DOI: 10.1021/Acs.Jctc.0C00163  0.323
2019 Nam K, Karplus M. Insights into the origin of the high energy-conversion efficiency of F-ATPase. Proceedings of the National Academy of Sciences of the United States of America. PMID 31341091 DOI: 10.1073/Pnas.1906816116  0.301
2018 Das S, Nam K, Major DT. Rapid Convergence of Energy and Free Energy Profiles with QM Size in QM/MM Simulations of Proton Transfer in DNA. Journal of Chemical Theory and Computation. PMID 29446946 DOI: 10.1021/Acs.Jctc.7B00964  0.371
2017 Mishra Y, Hall M, Locmelis R, Nam K, Söderberg CAG, Storm P, Chaurasia N, Rai LC, Jansson S, Schröder WP, Sauer UH. Active-site plasticity revealed in the asymmetric dimer of AnPrx6 the 1-Cys peroxiredoxin and molecular chaperone from Anabaena sp. PCC 7210. Scientific Reports. 7: 17151. PMID 29215017 DOI: 10.1038/S41598-017-17044-3  0.355
2017 Li Y, Nam K. Dynamic, structural and thermodynamic basis of insulin-like growth factor 1 kinase allostery mediated by activation loop phosphorylation. Chemical Science. 8: 3453-3464. PMID 28507717 DOI: 10.1039/C7Sc00055C  0.33
2016 Ovchinnikov V, Nam K, Karplus M. A Simple and Accurate Method to Calculate Free Energy Profiles and Reaction Rates from Restrained Molecular Simulations of Diffusive Processes. The Journal of Physical Chemistry. B. PMID 27135391 DOI: 10.1021/Acs.Jpcb.6B02139  0.353
2015 Ojeda-May P, Li Y, Ovchinnikov V, Nam K. Role of Protein Dynamics in Allosteric Control of the Catalytic Phosphoryl Transfer of Insulin Receptor Kinase. Journal of the American Chemical Society. PMID 26374925 DOI: 10.1021/Jacs.5B07996  0.375
2014 Nam K. Acceleration of Ab Initio QM/MM Calculations under Periodic Boundary Conditions by Multiscale and Multiple Time Step Approaches. Journal of Chemical Theory and Computation. 10: 4175-83. PMID 26588116 DOI: 10.1021/Ct5005643  0.339
2014 Nam K, Pu J, Karplus M. Trapping the ATP binding state leads to a detailed understanding of the F1-ATPase mechanism. Proceedings of the National Academy of Sciences of the United States of America. 111: 17851-6. PMID 25453082 DOI: 10.1073/Pnas.1419486111  0.343
2014 Koag MC, Nam K, Lee S. The spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase β. Nucleic Acids Research. 42: 11233-45. PMID 25200079 DOI: 10.1093/Nar/Gku789  0.336
2014 Doron D, Kohen A, Nam K, Major DT. How Accurate Are Transition States from Simulations of Enzymatic Reactions? Journal of Chemical Theory and Computation. 10: 1863-1871. PMID 24860275 DOI: 10.1021/Ct5000742  0.384
2013 Nam K. Acceleration of Semiempirical Quantum Mechanical Calculations by Extended Lagrangian Molecular Dynamics Approach. Journal of Chemical Theory and Computation. 9: 3393-403. PMID 26584095 DOI: 10.1021/Ct400117K  0.353
2013 Huang Y, Nam K, Westlund PO. The water R1(ω) NMRD profiles of a hydrated protein from molecular dynamics simulation. Physical Chemistry Chemical Physics : Pccp. 15: 14089-97. PMID 23868443 DOI: 10.1039/C3Cp51147B  0.3
2012 Crenshaw CM, Nam K, Oo K, Kutchukian PS, Bowman BR, Karplus M, Verdine GL. Enforced presentation of an extrahelical guanine to the lesion recognition pocket of human 8-oxoguanine glycosylase, hOGG1. The Journal of Biological Chemistry. 287: 24916-28. PMID 22511791 DOI: 10.1074/Jbc.M111.316497  0.35
2012 Qi Y, Nam K, Spong MC, Banerjee A, Sung RJ, Zhang M, Karplus M, Verdine GL. Strandwise translocation of a DNA glycosylase on undamaged DNA. Proceedings of the National Academy of Sciences of the United States of America. 109: 1086-91. PMID 22219368 DOI: 10.1073/Pnas.1111237108  0.313
2011 Fischer S, Olsen KW, Nam K, Karplus M. Unsuspected pathway of the allosteric transition in hemoglobin. Proceedings of the National Academy of Sciences of the United States of America. 108: 5608-13. PMID 21415366 DOI: 10.1073/Pnas.1011995108  0.312
2010 Qi Y, Spong MC, Nam K, Karplus M, Verdine GL. Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM. The Journal of Biological Chemistry. 285: 1468-78. PMID 19889642 DOI: 10.1074/Jbc.M109.069799  0.325
2009 Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S, Karplus M, Verdine GL. Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme. Nature. 462: 762-6. PMID 20010681 DOI: 10.1038/Nature08561  0.321
2009 Nam K, Verdine GL, Karplus M. Analysis of an anomalous mutant of MutM DNA glycosylase leads to new insights into the catalytic mechanism. Journal of the American Chemical Society. 131: 18208-9. PMID 19961158 DOI: 10.1021/Ja907544B  0.394
2009 Nam K, Verdine GL, Karplus M. Molecular Mechanism of the Acceleration of the Damaged Base Extrusion and its Recognition by Bacterial MutM DNA Glycosylase: Free Energy Simulation Studies Biophysical Journal. 96: 342a. DOI: 10.1016/J.Bpj.2008.12.1716  0.387
2008 Nam K, Gao J, York DM. Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases. Rna (New York, N.Y.). 14: 1501-7. PMID 18566190 DOI: 10.1261/Rna.863108  0.391
2008 Nam K, Gao J, York DM. Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis. Journal of the American Chemical Society. 130: 4680-91. PMID 18345664 DOI: 10.1021/Ja0759141  0.384
2007 Nam K, Cui Q, Gao J, York DM. Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions:  H, O, and P Atoms. Journal of Chemical Theory and Computation. 3: 486-504. PMID 26637030 DOI: 10.1021/Ct6002466  0.354
2006 Gao J, Ma S, Major DT, Nam K, Pu J, Truhlar DG. Mechanisms and free energies of enzymatic reactions. Chemical Reviews. 106: 3188-209. PMID 16895324 DOI: 10.1021/Cr050293K  0.396
2006 Giese TJ, Gregersen BA, Liu Y, Nam K, Mayaan E, Moser A, Range K, Faza ON, Lopez CS, de Lera AR, Schaftenaar G, Lopez X, Lee TS, Karypis G, York DM. QCRNA 1.0: a database of quantum calculations for RNA catalysis. Journal of Molecular Graphics & Modelling. 25: 423-33. PMID 16580853 DOI: 10.1016/J.Jmgm.2006.02.011  0.314
2005 Nam K, Gao J, York DM. An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations. Journal of Chemical Theory and Computation. 1: 2-13. PMID 26641110 DOI: 10.1021/Ct049941I  0.372
2004 Nam K, Prat-Resina X, Garcia-Viloca M, Devi-Kesavan LS, Gao J. Dynamics of an enzymatic substitution reaction in haloalkane dehalogenase. Journal of the American Chemical Society. 126: 1369-76. PMID 14759194 DOI: 10.1021/Ja039093L  0.359
2004 Garcia-Viloca M, Nam K, Alhambra C, Gao J. Solvent and Protein Effects on the Vibrational Frequency Shift and Energy Relaxation of the Azide Ligand in Carbonic Anhydrase The Journal of Physical Chemistry B. 108: 13501-13512. DOI: 10.1021/Jp047526G  0.323
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