Search Results - "Koefinger, Juergen"

Hydrodynamics of Diffusion in Lipid Membrane Simulations by Vögele, Martin, Köfinger, Jürgen, Hummer, Gerhard

“…By performing molecular dynamics simulations with up to 132 million coarse-grained particles in half-micron sized boxes, we show that hydrodynamics…”
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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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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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CADISHI: Fast parallel calculation of particle-pair distance histograms on CPUs and GPUs by Reuter, Klaus, Köfinger, Jürgen

“…We report on the design, implementation, optimization, and performance of the CADISHI software package, which calculates histograms of pair-distances of…”
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Quantifying Protein-Protein Interactions in Molecular Simulations by Jost Lopez, Alfredo, Quoika, Patrick K, Linke, Max, Hummer, Gerhard, Köfinger, Jürgen

“…Interactions among proteins, nucleic acids, and other macromolecules are essential for their biological functions and shape the physicochemcial properties of…”
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Inferring Structural Ensembles of Flexible and Dynamic Macromolecules Using Bayesian, Maximum Entropy, and Minimal-Ensemble Refinement Methods by Köfinger, Jürgen, Różycki, Bartosz, Hummer, Gerhard

“…The flexible and dynamic nature of biomolecules and biomolecular complexes is essential for many cellular functions in living organisms but poses a challenge…”
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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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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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Single-file water in nanopores by Köfinger, Jürgen, Hummer, Gerhard, Dellago, Christoph

“…Water molecules confined to pores with sub-nanometre diameters form single-file hydrogen-bonded chains. In such nanoscale confinement, water has unusual…”
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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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SAXS/WAXS Intensities and Pair-Distance Distribution Functions from Molecular Dynamics Simulations by Koefinger, Juergen, Hummer, Gerhard

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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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Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation by Barends, Thomas R. M., Foucar, Lutz, Ardevol, Albert, Nass, Karol, Aquila, Andrew, Botha, Sabine, Doak, R. Bruce, Falahati, Konstantin, Hartmann, Elisabeth, Hilpert, Mario, Heinz, Marcel, Hoffmann, Matthias C., Köfinger, Jürgen, Koglin, Jason E., Kovacsova, Gabriela, Liang, Mengning, Milathianaki, Despina, Lemke, Henrik T., Reinstein, Jochen, Roome, Christopher M., Shoeman, Robert L., Williams, Garth J., Burghardt, Irene, Hummer, Gerhard, Boutet, Sébastien, Schlichting, Ilme

“…The hemoprotein myoglobin is a model system for the study of protein dynamics. We used time-resolved serial femtosecond crystallography at an x-ray…”
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From integrative atomic-resolution ensembles of disordered proteins to simulations of phase-separated condensates by Stelzl, Lukas S., Pietrek, Lisa M., Ping, Xiaofei, Holla, Andrea, Sikora, Mateusz, Koefinger, Juergen, Dormann, Dorothee, Schuler, Benjamin, Zweckstetter, Markus, Hummer, Gerhard

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Simple and Efficient Calculation of Scattering Intensities of Proteins in Solution from Atomistically Detailed Structures by Koefinger, Juergen, Hummer, Gerhard

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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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