Publications
115 results
115 results
2013
Kalgin I, Caflisch A, Chekmarev S, Karplus M. New Insights into the Folding of a β-Sheet Miniprotein in a Reduced Space of Collective Hydrogen Bond Variables: Application to a Hydrodynamic Analysis of the Folding Flow. J. Phys. Chem. B. 2013;117(20):6092–6105.
Kalgin I, Caflisch A, Chekmarev S, Karplus M. New Insights into the Folding of a β-Sheet Miniprotein in a Reduced Space of Collective Hydrogen Bond Variables: Application to a Hydrodynamic Analysis of the Folding Flow. J. Phys. Chem. B. 2013;117(20):6092–6105.
Calimet N, Simoes M, Changeux J-P, Karplus M, Taly A, Cecchini M. A Gating Mechanism of Pentameric Ligand-gated Ion Channels. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(42):E3987-E3996.
Calimet N, Simoes M, Changeux J-P, Karplus M, Taly A, Cecchini M. A Gating Mechanism of Pentameric Ligand-gated Ion Channels. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(42):E3987-E3996.
Ovchinnikov V, Cecchini M, Karplus M. A Simplified Confinement Method for Calculating Absolute Free Energies and Free Energy and Entropy Differences. J. Phys. Chem. B. 2013;117(3):750–762.
Ovchinnikov V, Cecchini M, Karplus M. A Simplified Confinement Method for Calculating Absolute Free Energies and Free Energy and Entropy Differences. J. Phys. Chem. B. 2013;117(3):750–762.
Zheng G, Schaefer M, Karplus M. Hemoglobin Bohr Effects: Atomic Origin of the Histidine Residue Contributions. Biochemistry. 2013;52(47):8539–8555.
Zheng G, Schaefer M, Karplus M. Hemoglobin Bohr Effects: Atomic Origin of the Histidine Residue Contributions. Biochemistry. 2013;52(47):8539–8555.
2012
Crenshaw C, Nam K, Oo K, Kutchukian P, Bowman B, Karplus M, Verdine G. Enforced Presentation of an Extrahelical Guanine to the Lesion Recognition Pocket of Human 8-Oxoguanine Glycosylase, hOGG1. Journal of Biological Chemistry. 2012;287(30):24916–24928.
Crenshaw C, Nam K, Oo K, Kutchukian P, Bowman B, Karplus M, Verdine G. Enforced Presentation of an Extrahelical Guanine to the Lesion Recognition Pocket of Human 8-Oxoguanine Glycosylase, hOGG1. Journal of Biological Chemistry. 2012;287(30):24916–24928.
Karthikeyan G, Zambaldo C, Barluenga S, Zoete V, Karplus M, Winssinger N. Asymmetric Synthesis of Pochonin E and F, Revision of Their Proposed Structure, and Their Conversion to Potent Hsp90 Inhibitors. Chemistry - A European Journal. 2012;18(29):8978–8986.
Karthikeyan G, Zambaldo C, Barluenga S, Zoete V, Karplus M, Winssinger N. Asymmetric Synthesis of Pochonin E and F, Revision of Their Proposed Structure, and Their Conversion to Potent Hsp90 Inhibitors. Chemistry - A European Journal. 2012;18(29):8978–8986.
Ovchinnikov V, Karplus M. Analysis and Elimination of a Bias in Targeted Molecular Dynamics Simulations of Conformational Transitions: Application to Calmodulin. J. Phys. Chem. B. 2012;116(29):8584–8603.
Ovchinnikov V, Karplus M. Analysis and Elimination of a Bias in Targeted Molecular Dynamics Simulations of Conformational Transitions: Application to Calmodulin. J. Phys. Chem. B. 2012;116(29):8584–8603.
Qi Y, Nam K, Spong M, Banerjee A, Sung R-J, Zhang M, Karplus M, Verdine G. Strandwise translocation of a DNA glycosylase on undamaged DNA. Proceedings of the National Academy of Sciences of the United States of America. 2012;109(4):1086–1091.
Qi Y, Nam K, Spong M, Banerjee A, Sung R-J, Zhang M, Karplus M, Verdine G. Strandwise translocation of a DNA glycosylase on undamaged DNA. Proceedings of the National Academy of Sciences of the United States of America. 2012;109(4):1086–1091.
2011
Ovchinnikov V, Cecchini M, Vanden-Eijnden E, Karplus M. A Conformational Transition in the Myosin VI Converter Contributes to the Variable Step Size. Biophysical Journal. 2011;101(10):2436–2444.
Ovchinnikov V, Cecchini M, Vanden-Eijnden E, Karplus M. A Conformational Transition in the Myosin VI Converter Contributes to the Variable Step Size. Biophysical Journal. 2011;101(10):2436–2444.
Zheng G, Niklasson A, Karplus M. Lagrangian formulation with dissipation of Born-Oppenheimer molecular dynamics using the density-functional tight-binding method. J. Chem. Phys. 2011;135(4):044122/1–044122/17.
Zheng G, Niklasson A, Karplus M. Lagrangian formulation with dissipation of Born-Oppenheimer molecular dynamics using the density-functional tight-binding method. J. Chem. Phys. 2011;135(4):044122/1–044122/17.
Karplus M. Behind the folding funnel diagram. Nature Chemical Biology. 2011;7(7):401–404.
Karplus M. Behind the folding funnel diagram. Nature Chemical Biology. 2011;7(7):401–404.
Luo G-B, Karplus M. Determining the Conformational Change that Accompanies Donor-Acceptor Distance Fluctuations: An Umbrella Sampling Analysis. J. Phys. Chem. B. 2011;115(24):7991–7995.
Luo G-B, Karplus M. Determining the Conformational Change that Accompanies Donor-Acceptor Distance Fluctuations: An Umbrella Sampling Analysis. J. Phys. Chem. B. 2011;115(24):7991–7995.