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393 results for “Molecular dynamics simulations”
Molecular dynamics simulations of intrinsically disordered proteins p53TAD and Pup
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Molecular dynamics simulation data of designed stapled α-helix
<p>Raw simulations data (protein only) and simulation set-up files of designed stapled α-helix peptides. More details can be found in this paper: </p> <p>Arusha Acharyya*, Yunhui Ge*, Haifan Wu*, William DeGrado, Vincent Voelz, Feng Gai. <a href="https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.8b12220"><em>Exposing the Nucleation Site in α-Helix Folding: A Joint Experimental and Simulation Study.</em></a><em> </em>J. Phys. Chem. B., 2019, 123 (8), pp 1797-1807 (* shared first author)</p>
Molecular dynamics simulation data of designed cyclic peptide - ligand 4 (receptor-ligand bound)
<p>Trajectories of receptor-ligand bound simulation and simulation set-up files of designed cyclic peptide as MDM2 binders. This dataset contains simulations of ligand 4. Due to the file size limitation, ligand 1-3 data and simulation set-up files can be found here: http://doi.org/10.5281/zenodo.3780463<br> The original paper of these designed cyclic peptide: Danelius, E., Pettersson, M., Bred, M., Min, J., Waddell, M. B., Guy, R. K., et al. (2016). Flexibility is important for inhibition of the MDM2/p53 protein–protein interaction by cyclic β-hairpins. <em>Org. Biomol. Chem.</em>, <em>14</em>(44), 10386–10393. http://doi.org/10.1039/C6OB01510G</p>
Molecular dynamics simulation data of designed cyclic peptide - ligand 1-3 (receptor-ligand bound)
<p>Trajectories of receptor-ligand bound simulation and simulation set-up files of designed cyclic peptide as MDM2 binders. This dataset contains simulations of ligand 1-3. Ligand 4 data can be found here: http://doi.org/10.5281/zenodo.3782629<br> The original paper of these designed cyclic peptide: Danelius, E., Pettersson, M., Bred, M., Min, J., Waddell, M. B., Guy, R. K., et al. (2016). Flexibility is important for inhibition of the MDM2/p53 protein–protein interaction by cyclic β-hairpins. <em>Org. Biomol. Chem.</em>, <em>14</em>(44), 10386–10393. http://doi.org/10.1039/C6OB01510G</p>
Molecular dynamics simulation data of regulatory ACT domain dimer of human phenylalanine hydroxylase (PAH) (dimer only)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer. Simulation starts from the crystal pose (PDB: 5FII) and is motivated by this paper:</p> <p>Yunhui Ge, Elias Borne, Shannon Stewart, Michael R. Hansen, Emilia C. Arturo, Eileen K. Jaffe and Vincent A. Voelz. <a href="http://www.jbc.org/content/293/51/19532"><em>Simulation of the regulatory ACT domain of human PAH unveil the mechanism of phenylalanine binding.</em></a> J. Biol. Chem., 2018, 293(51), pp 19532-19543</p>
Molecular recognition and dynamics of linear poly-ubiquitins: integrating coarse-grain simulations and experiments
<p>Poly-ubiquitin chains are flexible multidomain proteins, whose conformational dynamics enable their molecular recognition by a large number of partners in multiple biological pathways. By using alternative linkage, it is possible to obtain poly-ubiquitin molecules with different dynamical properties. This flexibility is further increased by the possibility to tune the length of poly-ubiquitin chains. Characterizing the dynamics of poly-ubiquitins as a function of their length is thus relevant to understand their biology. Structural characterization of poly-ubiquitin conformational dynamics is challenging both experimentally and computationally due to increasing system size and conformational variability. Here, by developing highly efficient and accurate small-angle X-ray scattering driven Martini coarse-grain simulations, we characterize the dynamics of linear M1-linked di-, tri- and tetra-ubiquitin chains. Our data show that the behavior of the di-ubiquitin subunits is independent of the presence of additional ubiquitin modules. We propose that the conformational space sampled by linear poly-ubiquitins, in general, may follow a simple self-avoiding polymer model. These results, combined with experimental data from small angle X-ray scattering, biophysical techniques and additional simulations show that binding of NEMO, a central regulator in the NF-κB pathway, to linear poly-ubiquitin obeys a 2:1 (NEMO:poly-ubiquitin) stoichiometry in solution, even in the context of four ubiquitin units. Eventually, we show how the conformational properties of long poly-ubiquitins may modulate the binding with their partners in a length-dependent manner.</p>
Supplementary Information for Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS
<p>Supplementary information for<br> Páll, S., Zhmurov, A., Bauer, P., Abraham, M., Lundborg, M., Gray, A., Hess, B, & Lindahl, E.. (2020). Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS. The Journal of Chemical Physics, 2020</p> <p>Contains benchmark methodology description as well as all inputs used in the application performance benchmarks included the paper.</p>
Molecular dynamics simulations data for "Bayesian unsupervised learning reveals hidden structure in concentrated electrolytes".
<p>Molecular dynamics simulation data created and used in "Bayesian unsupervised learning reveals hidden structure in concentrated electrolytes".</p> <p> </p>
Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"
<p>Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 1H-13C solid-state NMR and molecular dynamics simulations" Langmuir 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r</p> <p>System: 70 wt% C12E5, T=298K</p> <p>Other files available: http://dx.doi.org/10.6084/m9.figshare.861071</p>
Molecular dynamics simulations of the temperature-induced unfolding of crambin follow the Arrhenius equation.
<p>These are the output files from the Gromacs simulations of the temperature induced unfolding of crambin.</p>
Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"
<p>Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 1H-13C solid-state NMR and molecular dynamics simulations" Langmuir 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r</p> <p>System: 70 wt% C12E5, T=320K</p> <p>Other files available: http://dx.doi.org/10.6084/m9.figshare.861071</p>
Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"
<p>Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 1H-13C solid-state NMR and molecular dynamics simulations" Langmuir 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r</p> <p>System: 70 wt% C12E5, T=333K</p> <p>Other files available: http://dx.doi.org/10.6084/m9.figshare.861071</p>
Molecular dynamics simulations of the temperature-induced unfolding of crambin follow the Arrhenius equation.
<p>These are the SPSS files for the statistical analysis of the temperature induced unfolding of crambin.</p>
Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"
<p>Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 1H-13C solid-state NMR and molecular dynamics simulations" Langmuir 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r</p> <p>System: 60 wt% C12E5, T=333K</p> <p>Other files available: http://dx.doi.org/10.6084/m9.figshare.861071</p>
Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"
<p>Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 1H-13C solid-state NMR and molecular dynamics simulations" Langmuir 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r</p> <p>System: 60 wt% C12E5, T=320K</p> <p>Other files available: http://dx.doi.org/10.6084/m9.figshare.861071</p>
Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"
<p>Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 1H-13C solid-state NMR and molecular dynamics simulations" Langmuir 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r</p> <p>System: 60 wt% C12E5, T=298K</p> <p>Other files available: http://dx.doi.org/10.6084/m9.figshare.861071</p>
Molecular dynamics simulation trajectory of a cationic lipid bilayer: 6/94 mol% DMTAP/DMPC
<p><strong>System: </strong>Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 6 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 94 mol-%) lipids in water.</p> <p><strong>Number of DMPC: </strong>120.<br> <strong>Number of DMTAP:</strong> 8.<br> <strong>Number of Cl<sup>-</sup>-ions:</strong> 8.<br> <strong>Number of waters:</strong> 5099.</p> <p><strong>Lipid model:</strong> 'Berger' united-atom [<em>Biophys. J.</em> <strong>72</strong> 2002 (1997)] with DMTAP modification by Gurtovenko et al. [<em>Biophys. J. </em><strong>86</strong> 3461 (2004)].<br> <strong>Water model:</strong> SPC [In <em>Intermolecular Forces,</em> ed. Pullman. 331 (1981)].</p> <p><strong>Simulation engine:</strong> Gromacs 3.x [www.gromacs.org]</p> <p><strong>Trajectory length:</strong> 109 ns.<br> <strong>Previously equilibrated for:</strong> 32 ns.<br> <strong>Sampling rate:</strong> every 10 ps.</p> <p><strong>Time integration step:</strong> 2 fs.</p> <p><strong>Thermodynamic ensemble:</strong> NpT. <br> <strong>Temperature coupling:</strong> 'Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with lipids and water coupled separately at T = 323 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with xy and z coupled separately at p = 1.0 bar.</p> <p><strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993); <em>J. Chem. Phys.</em> <strong>103</strong> 8577 (1995)], real-space cutoff at 1.0 nm.<br> <strong>Van der Waals:</strong> Truncated at 1.0 nm.</p> <p><strong>Constraints: </strong>Covalent bond lengths in lipids using LINCS [<em>J. Comput. Chem.</em> <strong>18</strong> 1463 (1997)], in water using SETTLE [J. Comput. Chem. <strong>13</strong> 952 (1992)].</p> <p><strong>Used in publications: </strong>[1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". <em>J. Phys. Chem. B</em> <strong>113</strong> 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.</p>
Molecular dynamics simulation trajectory of a fully hydrated DMPC lipid bilayer
<p><strong>System: </strong>DMPC (dimyristoylphosphatidylcholine) bilayer in water.</p> <p><strong>Number of lipids: </strong>128.<br> <strong>Number of waters:</strong> 5097.</p> <p><strong>Lipid model:</strong> 'Berger' united-atom [<em>Biophys. J.</em> <strong>72</strong> 2002 (1997)].<br> <strong>Water model:</strong> SPC [In <em>Intermolecular Forces,</em> ed. Pullman. 331 (1981)].</p> <p><strong>Simulation engine:</strong> Gromacs 3.x [www.gromacs.org]</p> <p><strong>Trajectory length:</strong> 110 ns.<br> <strong>Previously equilibrated for:</strong> 20 ns.<br> <strong>Sampling rate:</strong> every 10 ps.</p> <p><strong>Time integration step:</strong> 2 fs.</p> <p><strong>Thermodynamic ensemble:</strong> NpT. <br> <strong>Temperature coupling:</strong> 'Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with lipids and water coupled separately at T = 323 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with xy and z coupled separately at p = 1.0 bar.</p> <p><strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993); <em>J. Chem. Phys.</em> <strong>103</strong> 8577 (1995)], real-space cutoff at 1.0 nm.<br> <strong>Van der Waals:</strong> Truncated at 1.0 nm.</p> <p><strong>Constraints: </strong>Covalent bond lengths in lipids using LINCS [<em>J. Comput. Chem.</em> <strong>18</strong> 1463 (1997)], in water using SETTLE [J. Comput. Chem. <strong>13</strong> 952 (1992)].</p> <p><strong>Used in publications: </strong>[1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". <em>J. Phys. Chem. B</em> <strong>113</strong> 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.</p>
Molecular dynamics simulation trajectory of a cationic lipid bilayer: 50/50 mol% DMTAP/DMPC in 0.5 M NaCl
<p><strong>System: </strong>Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 50 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 50 mol-%) lipids in 0.5 M NaCl solution.</p> <p><strong>Number of DMPC:</strong> 64.<br> <strong>Number of DMTAP:</strong> 64.<br> <strong>Number of Na<sup>+</sup>-ions:</strong> 48.<br> <strong>Number of Cl<sup>-</sup>-ions:</strong> 112.<br> <strong>Number of waters:</strong> 5240.</p> <p><strong>Lipid model:</strong> 'Berger' united-atom [<em>Biophys. J.</em> <strong>72</strong> 2002 (1997)] with DMTAP modification by Gurtovenko et al. [<em>Biophys. J. </em><strong>86</strong> 3461 (2004)].<br> <strong>Water model:</strong> SPC [In <em>Intermolecular Forces,</em> ed. Pullman. 331 (1981)].</p> <p><strong>Simulation engine:</strong> Gromacs 3.x [www.gromacs.org]</p> <p><strong>Trajectory length:</strong> 179 ns.<br> <strong>Previously equilibrated for:</strong> 21 ns.<br> <strong>Sampling rate:</strong> every 10 ps.</p> <p><strong>Time integration step:</strong> 2 fs.</p> <p><strong>Thermodynamic ensemble:</strong> NpT. <br> <strong>Temperature coupling:</strong> 'Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with lipids and water coupled separately at T = 323 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with xy and z coupled separately at p = 1.0 bar.</p> <p><strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993); <em>J. Chem. Phys.</em> <strong>103</strong> 8577 (1995)], real-space cutoff at 1.0 nm.<br> <strong>Van der Waals:</strong> Truncated at 1.0 nm.</p> <p><strong>Constraints: </strong>Covalent bond lengths in lipids using LINCS [<em>J. Comput. Chem.</em> <strong>18</strong> 1463 (1997)], in water using SETTLE [J. Comput. Chem. <strong>13</strong> 952 (1992)].</p> <p><strong>Used in publications: </strong>[1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". <em>J. Phys. Chem. B</em> <strong>113</strong> 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.</p>
Molecular dynamics simulation trajectory of a cationic lipid bilayer: 50/50 mol% DMTAP/DMPC in 1.0 M NaCl
<p><strong>System: </strong>Symmetric bilayer of cationic DMTAP (dimyristoyltrimethylammoniumpropane, 50 mol-%) and zwitterionic DMPC (dimyristoylphosphatidylcholine, 50 mol-%) lipids in 1.0 M NaCl solution.</p> <p><strong>Number of DMPC:</strong> 64.<br> <strong>Number of DMTAP:</strong> 64.<br> <strong>Number of Na<sup>+</sup>-ions:</strong> 94.<br> <strong>Number of Cl<sup>-</sup>-ions:</strong> 158.<br> <strong>Number of waters:</strong> 5148.</p> <p><strong>Lipid model:</strong> 'Berger' united-atom [<em>Biophys. J.</em> <strong>72</strong> 2002 (1997)] with DMTAP modification by Gurtovenko et al. [<em>Biophys. J. </em><strong>86</strong> 3461 (2004)].<br> <strong>Water model:</strong> SPC [In <em>Intermolecular Forces,</em> ed. Pullman. 331 (1981)].</p> <p><strong>Simulation engine:</strong> Gromacs 3.x [www.gromacs.org]</p> <p><strong>Trajectory length:</strong> 170 ns.<br> <strong>Previously equilibrated for:</strong> 21 ns.<br> <strong>Sampling rate:</strong> every 10 ps.</p> <p><strong>Time integration step:</strong> 2 fs.</p> <p><strong>Thermodynamic ensemble:</strong> NpT. <br> <strong>Temperature coupling:</strong> 'Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with lipids and water coupled separately at T = 323 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984)] with xy and z coupled separately at p = 1.0 bar.</p> <p><strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993); <em>J. Chem. Phys.</em> <strong>103</strong> 8577 (1995)], real-space cutoff at 1.0 nm.<br> <strong>Van der Waals:</strong> Truncated at 1.0 nm.</p> <p><strong>Constraints: </strong>Covalent bond lengths in lipids using LINCS [<em>J. Comput. Chem.</em> <strong>18</strong> 1463 (1997)], in water using SETTLE [J. Comput. Chem. <strong>13</strong> 952 (1992)].</p> <p><strong>Used in publications: </strong>[1] Markus S. Miettinen, Andrey A. Gurtovenko, Ilpo Vattulainen, and Mikko Karttunen: "Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions". <em>J. Phys. Chem. B</em> <strong>113</strong> 9226 (2009). DOI: 10.1021/jp810233q. [2] Markus S. Miettinen: "Computational Modeling of Cationic Lipid Bilayers in Saline Solutions". PhD Thesis. Aalto University School of Science and Technology, Helsinki, Finland. (2010). ISBN 978-952-60-3194-1.</p>
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