Search Results - "Köfinger, Jürgen"

Bayesian ensemble refinement by replica simulations and reweighting by Hummer, Gerhard, Köfinger, Jürgen

“…We describe different Bayesian ensemble refinement methods, examine their interrelation, and discuss their practical application. With ensemble refinement, the…”
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Empirical optimization of molecular simulation force fields by Bayesian inference by Köfinger, Jürgen, Hummer, Gerhard

“…The demands on the accuracy of force fields for classical molecular dynamics simulations are steadily growing as larger and more complex systems are studied…”
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Finite-Size-Corrected Rotational Diffusion Coefficients of Membrane Proteins and Carbon Nanotubes from Molecular Dynamics Simulations by Vögele, Martin, Köfinger, Jürgen, Hummer, Gerhard

“…We investigate system-size effects on the rotational diffusion of membrane proteins and other membrane-embedded molecules in molecular dynamics simulations. We…”
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Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations by Linke, Max, Köfinger, Jürgen, Hummer, Gerhard

“…We present a method to calculate the fully anisotropic rotational diffusion tensor from molecular dynamics simulations. Our approach is based on fitting the…”
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Rotational Diffusion Depends on Box Size in Molecular Dynamics Simulations by Linke, Max, Köfinger, Jürgen, Hummer, Gerhard

“…We show that the rotational dynamics of proteins and nucleic acids determined from molecular dynamics simulations under periodic boundary conditions suffer…”
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Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure by Stelzl, Lukas S, Pietrek, Lisa M, Holla, Andrea, Oroz, Javier, Sikora, Mateusz, Köfinger, Jürgen, Schuler, Benjamin, Zweckstetter, Markus, Hummer, Gerhard

“…The paradigmatic disordered protein tau plays an important role in neuronal function and neurodegenerative diseases. To disentangle the factors controlling the…”
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Molecular dynamics simulations of carbon nanotube porins in lipid bilayers by Vögele, Martin, Köfinger, Jürgen, Hummer, Gerhard

“…Artificial channels made of carbon nanotube (CNT) porins are promising candidates for applications in filtration and molecular delivery devices. Their…”
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Efficient Ensemble Refinement by Reweighting by Köfinger, Jürgen, Stelzl, Lukas S, Reuter, Klaus, Allande, César, Reichel, Katrin, Hummer, Gerhard

“…Ensemble refinement produces structural ensembles of flexible and dynamic biomolecules by integrating experimental data and molecular simulations. Here we…”
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Fragment Binding Pose Predictions Using Unbiased Simulations and Markov-State Models by Linker, Stephanie Maria, Magarkar, Aniket, Köfinger, Jürgen, Hummer, Gerhard, Seeliger, Daniel

“…Predicting the costructure of small-molecule ligands and their respective target proteins has been a long-standing problem in drug discovery. For weak binding…”
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Macroscopically ordered water in nanopores by Köfinger, Jürgen, Hummer, Gerhard, Dellago, Christoph

“…Water confined into the interior channels of narrow carbon nanotubes or transmembrane proteins forms collectively oriented molecular wires held together by…”
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Precision DEER Distances from Spin-Label Ensemble Refinement by Reichel, Katrin, Stelzl, Lukas S, Köfinger, Jürgen, Hummer, Gerhard

“…Double electron–electron resonance (DEER) experiments probe nanometer-scale distances in spin-labeled proteins and nucleic acids. Rotamer libraries of the…”
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Nanoporous Membranes of Densely Packed Carbon Nanotubes Formed by Lipid-Mediated Self-Assembly by Vögele, Martin, Köfinger, Jürgen, Hummer, Gerhard

“…Nanofiltration technology faces the competing challenges of achieving high fluid flux through uniformly narrow pores of a mechanically and chemically stable…”
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Carbon Nanotubes Mediate Fusion of Lipid Vesicles by Bhaskara, Ramachandra M, Linker, Stephanie M, Vögele, Martin, Köfinger, Jürgen, Hummer, Gerhard

“…The fusion of lipid membranes is opposed by high energetic barriers. In living organisms, complex protein machineries carry out this biologically essential…”
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Orientational dynamics and dielectric response of nanopore water by Köfinger, Jürgen, Dellago, Christoph

“…We present numerical calculations, simulation results, and analytical considerations for the frequency-dependent dielectric constant of single-file water in…”
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The statistics of electric field fluctuations in liquid water by Reischl, Bernhard, Köfinger, Jürgen, Dellago, Christoph

“…Electric field fluctuations play a major role in dissociation reactions in liquid water and determine its vibrational spectroscopic response. Here, we study…”
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Solution structure of the Atg1 complex: implications for the architecture of the phagophore assembly site by Köfinger, Jürgen, Ragusa, Michael J, Lee, Il-Hyung, Hummer, Gerhard, Hurley, James H

“…The biogenesis of autophagosomes commences at the phagophore assembly site (PAS), a protein-vesicle ultrastructure that is organized by the Atg1 complex. The…”
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Phase transition and interpore correlations of water in nanopore membranes by Menzl, Georg, Köfinger, Jürgen, Dellago, Christoph

“…Using computer simulations, we study a membrane of parallel narrow pores filled with one-dimensional wires of hydrogen-bonded water molecules. We show that…”
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Solution Structure and Conformational Flexibility of a Polyketide Synthase Module by Klaus, Maja, Rossini, Emanuele, Linden, Andreas, Paithankar, Karthik S, Zeug, Matthias, Ignatova, Zoya, Urlaub, Henning, Khosla, Chaitan, Köfinger, Jürgen, Hummer, Gerhard, Grininger, Martin

“…Polyketide synthases (PKSs) are versatile C-C bond-forming enzymes that are broadly distributed in bacteria and fungi. The polyketide compound family includes…”
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Atomic-resolution structural information from scattering experiments on macromolecules in solution by Köfinger, Jürgen, Hummer, Gerhard

“…The pair-distance distribution function (PDDF) contains all structural information probed in an elastic scattering experiment of macromolecular solutions…”
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Biasing the Center of Charge in Molecular Dynamics Simulations with Empirical Valence Bond Models: Free Energetics of an Excess Proton in a Water Droplet by Köfinger, Jürgen, Dellago, Christoph

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