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Zheng, Guishan; Schaefer, Michael; Karplus, Martin (2013) Hemoglobin Bohr effects: atomic origin of the histidine residue contributions. Biochemistry 52:8539-55
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Ovchinnikov, Victor; Cecchini, Marco; Karplus, Martin (2013) A simplified confinement method for calculating absolute free energies and free energy and entropy differences. J Phys Chem B 117:750-62
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Kalgin, Igor V; Caflisch, Amedeo; Chekmarev, Sergei F et al. (2013) New insights into the folding of a ?-sheet miniprotein in a reduced space of collective hydrogen bond variables: application to a hydrodynamic analysis of the folding flow. J Phys Chem B 117:6092-105
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Qi, Yan; Nam, Kwangho; Spong, Marie C et al. (2012) Strandwise translocation of a DNA glycosylase on undamaged DNA. Proc Natl Acad Sci U S A 109:1086-91
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Crenshaw, Charisse M; Nam, Kwangho; Oo, Kimberly et al. (2012) Enforced presentation of an extrahelical guanine to the lesion recognition pocket of human 8-oxoguanine glycosylase, hOGG1. J Biol Chem 287:24916-28
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Ovchinnikov, Victor; Karplus, Martin (2012) Analysis and elimination of a bias in targeted molecular dynamics simulations of conformational transitions: application to calmodulin. J Phys Chem B 116:8584-603
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Petrella, Robert J (2011) A versatile method for systematic conformational searches: application to CheY. J Comput Chem 32:2369-85
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Luo, Guobin; Karplus, Martin (2011) Determining the conformational change that accompanies donor-acceptor distance fluctuations: an umbrella sampling analysis. J Phys Chem B 115:7991-5
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Ovchinnikov, Victor; Trout, Bernhardt L; Karplus, Martin (2010) Mechanical coupling in myosin V: a simulation study. J Mol Biol 395:815-33
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Qi, Yan; Spong, Marie C; Nam, Kwangho et al. (2010) Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM. J Biol Chem 285:1468-78
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Showing the most recent 10 out of 22 publications
