# Publications Search Within Results Search Within Results search ## 115 results Show filters filter\_alt Sort by Year of PublicationAlphabetical A-Z sort ## 115 results Download 115 citations download- [BibTeX](/node/658456/export?format=bibtex) - [EndNote X3 XML](/node/658456/export?format=endnote8) - [EndNote 7 XML](/node/658456/export?format=endnote7) - [Endnote tagged](/node/658456/export?format=tagged) - [Marc](/node/658456/export?format=marc) - [PubMedId](/node/658456/export?format=pubmed_id) - [RIS](/node/658456/export?format=ris) ### 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](/publications/new-insights-folding-beta-sheet-miniprotein-reduced-space-collective). 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](/publications/new-insights-folding-beta-sheet-miniprotein-reduced-space-collective). J. Phys. Chem. B. 2013;117(20):6092–6105. - add\_circle do\_not\_disturb\_on Abstract A new anal. of the 20 μs equil. folding​/unfolding mol. dynamics simulations of the three-​stranded antiparallel β-​sheet miniprotein (beta3s) in implicit solvent is presented. The conformation space is reduced in dimensionality by introduction of linear... Calimet N, Simoes M, Changeux J-P, Karplus M, Taly A, Cecchini M. [A Gating Mechanism of Pentameric Ligand-​gated Ion Channels](/publications/gating-mechanism-pentameric-ligand-%E2%80%8Bgated-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](/publications/gating-mechanism-pentameric-ligand-%E2%80%8Bgated-ion-channels). Proceedings of the National Academy of Sciences of the United States of America. 2013;110(42):E3987-E3996. - add\_circle do\_not\_disturb\_on Abstract Pentameric ligand-​gated ion channels (pLGICs) play a central role in intercellular communication in the nervous system and are involved in fundamental processes such as attention, learning, and memory. They are oligomeric protein assemblies that convert... Ovchinnikov V, Cecchini M, Karplus M. [A Simplified Confinement Method for Calculating Absolute Free Energies and Free Energy and Entropy Differences](/publications/simplified-confinement-method-calculating-absolute-free-energies-and). 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](/publications/simplified-confinement-method-calculating-absolute-free-energies-and). J. Phys. Chem. B. 2013;117(3):750–762. - add\_circle do\_not\_disturb\_on Abstract A simple and robust formulation of the path-​independent confinement method for the calcn. of free energies is presented. The simplified confinement method (SCM) does not require matrix diagonalization or switching off the mol. force field, and has a... Zheng G, Schaefer M, Karplus M. [Hemoglobin Bohr Effects: Atomic Origin of the Histidine Residue Contributions](/publications/hemoglobin-bohr-effects-atomic-origin-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](/publications/hemoglobin-bohr-effects-atomic-origin-histidine-residue-contributions). Biochemistry. 2013;52(47):8539–8555. - add\_circle do\_not\_disturb\_on Abstract The Bohr effect in Hb, which refers to the dependence of the oxygen affinity on the pH, plays an important role in its cooperativity and physiol. function. The dominant contribution to the Bohr effect arises from the difference in the pKa values of His... ### 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](/publications/enforced-presentation-extrahelical-guanine-lesion-recognition-pocket). 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](/publications/enforced-presentation-extrahelical-guanine-lesion-recognition-pocket). Journal of Biological Chemistry. 2012;287(30):24916–24928. - add\_circle do\_not\_disturb\_on Abstract A poorly understood aspect of DNA repair proteins is their ability to identify exceedingly rare sites of damage embedded in a large excess of nearly identical undamaged DNA, while catalyzing repair only at the damaged sites. Progress toward understanding... 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](/publications/poorly-understood-aspect-dna-repair-proteins-their-ability-identify). 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](/publications/poorly-understood-aspect-dna-repair-proteins-their-ability-identify). Chemistry - A European Journal. 2012;18(29):8978–8986. - add\_circle do\_not\_disturb\_on Abstract A concise and modular synthesis of pochonin E and F, and their epimers at C-​6 established the correct stereochem. of these two natural products to be (6R)​. Several members of the pochonin family have been shown to bind the heat shock protein 90 (Hsp90)... Ovchinnikov V, Karplus M. [Analysis and Elimination of a Bias in Targeted Molecular Dynamics Simulations of Conformational Transitions: Application to Calmodulin](/publications/analysis-and-elimination-bias-targeted-molecular-dynamics-simulations). 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](/publications/analysis-and-elimination-bias-targeted-molecular-dynamics-simulations). J. Phys. Chem. B. 2012;116(29):8584–8603. - add\_circle do\_not\_disturb\_on Abstract The popular targeted mol. dynamics (TMD) method for generating transition paths in complex biomol. systems is revisited. In a typical TMD transition path, the large-​scale changes occur early and the small-​scale changes tend to occur later. As a result... 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](/publications/strandwise-translocation-dna-glycosylase-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](/publications/strandwise-translocation-dna-glycosylase-undamaged-dna). Proceedings of the National Academy of Sciences of the United States of America. 2012;109(4):1086–1091. - add\_circle do\_not\_disturb\_on Abstract Base excision repair of genotoxic nucleobase lesions in the genome is critically dependent upon the ability of DNA glycosylases to locate rare sites of damage embedded in a vast excess of undamaged DNA, using only thermal energy to fuel the search process... ### 2011 Ovchinnikov V, Cecchini M, Vanden-Eijnden E, Karplus M. [A Conformational Transition in the Myosin VI Converter Contributes to the Variable Step Size](/publications/conformational-transition-myosin-vi-converter-contributes-variable-step). 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](/publications/conformational-transition-myosin-vi-converter-contributes-variable-step). Biophysical Journal. 2011;101(10):2436–2444. - add\_circle do\_not\_disturb\_on Abstract Myosin VI (MVI) is a dimeric mol. motor that translocates backwards on actin filaments with a surprisingly large and variable step size, given its short lever arm. A recent x-​ray structure of MVI indicates that the large step size can be explained in... Zheng G, Niklasson A, Karplus M. [Lagrangian formulation with dissipation of Born-​Oppenheimer molecular dynamics using the density-​functional tight-​binding method](/publications/lagrangian-formulation-dissipation-born-%E2%80%8Boppenheimer-molecular-dynamics). 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](/publications/lagrangian-formulation-dissipation-born-%E2%80%8Boppenheimer-molecular-dynamics). J. Chem. Phys. 2011;135(4):044122/1–044122/17. - add\_circle do\_not\_disturb\_on Abstract An important element detg. the time requirements of Born-​Oppenheimer mol. dynamics (BOMD) is the convergence rate of the self-​consistent soln. of Roothaan equations (SCF)​. We show here that improved convergence and dynamics stability can be achieved... Karplus M. [Behind the folding funnel diagram](/publications/behind-folding-funnel-diagram). Nature Chemical Biology. 2011;7(7):401–404. Karplus M. [Behind the folding funnel diagram](/publications/behind-folding-funnel-diagram). Nature Chemical Biology. 2011;7(7):401–404. - add\_circle do\_not\_disturb\_on Abstract A review. This Commentary clarifies the meaning of the funnel diagram, which has been widely cited in papers on protein folding. To aid in the anal. of the funnel diagram, this Commentary reviews historical approaches to understanding the mechanism of... Luo G-B, Karplus M. [Determining the Conformational Change that Accompanies Donor-​Acceptor Distance Fluctuations: An Umbrella Sampling Analysis](/publications/determining-conformational-change-accompanies-donor-%E2%80%8Bacceptor-distance). 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](/publications/determining-conformational-change-accompanies-donor-%E2%80%8Bacceptor-distance). J. Phys. Chem. B. 2011;115(24):7991–7995. - add\_circle do\_not\_disturb\_on Abstract The response of a protein to variation of a specific coordinate can provide insights into the role of the overall architecture in the structural change. 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