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474 results for “molecular simulation”
Molecular dynamics simulation trajectory of an anionic lipid bilayer: 100 mol% POPS with Na+ counterions using Joung-Cheatham Ions
<p><strong>System:</strong> Symmetric bilayer of anionic POPS (palmitoyl-oleoyl-phosphatidylserine 100 mol-%) lipids with sodium (Na<sup>+</sup>) counter ions.</p> <p><strong>Number of POPS:</strong> 128.<br> <strong>Number of Na<sup>+</sup>-ions:</strong> 128.<br> <strong>Number of waters:</strong> 4480.</p> <p><strong>Lipid model:</strong> Amber Lipid 17 [IR Gould, AA Skjevik, CJ Dickson, BD Madej, RC Walker: "Lipid17: A Comprehensive AMBER Force Field for the Simulation of Zwitterionic and Anionic Lipids" in prep. (2018)].</p> <p><strong>Ion model:</strong> Joung–Cheatham [IS Joung, TE Cheatham III <em>J. Phys. Chem. B</em> <strong>112</strong> 9020 (2008)].</p> <p><strong>Water model:</strong> TIP3P [WL Jorgensen, J Chandrasekhar, JD Madura, RW Impey, ML Klein <em>J. Chem. Phys.</em> <strong>79</strong> 926 (1983)].</p> <p><strong>Simulation engine:</strong> Amber16 [DA Case et al. <em>AMBER 2017</em> UCSF (2017)].</p> <p><strong>Number of independent repeats per setup:</strong> 2.<br> <strong>Trajectory lengths per repeat:</strong> 400 ns + 100 ns.<br> <strong>Previously equilibrated for:</strong> 100 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> 'Langevin' at T = 298 K.<br> <strong>Pressure coupling:</strong> 'Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984); <em>J. Chem. Phys</em>. <strong>103</strong> 10252 (1995)] with <em>xy</em> and <em>z</em> coupled separately at p = 1.0 bar with no surface tension.</p> <p><strong>Electrostatics:</strong> PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993); <em>J. Chem. Theory Comput. </em><strong>9</strong> 3878 (2013)].<br> <strong>Van der Waals:</strong> Turned off between 1.0 nm and 1.5 nm.</p> <p><strong>Constraints:</strong> Lengths of covalent bonds involving Hydrogens in lipids using SHAKE [<em>J. Comput. Phys.</em> <strong>23</strong> 327 (1977)], in water using SETTLE [<em>J. Comput. Chem.</em> <strong>13</strong> 952 (1992)].</p> <p><strong>Used in publications:</strong> OHS Ollila et al. "NMRlipids IV: Headgroup & glycerol backbone structures, and cation binding in bilayers with PS lipids" in prep (2018).</p>
Molecular simulations of nanoscale two-phase Couette flow of a water-hexane system on a hydrophobic substrate
<p>This dataset contains the output of Molecular Dynamics simulations (MD) of two-phase Couette flow of water/hexane biphasic systems, in terms of density, velocity and temperature fields. Instructions on how to read and analyze the output files in the <code>.tar.gz</code> archives can be found in these previously-published datasets: <a href="https://doi.org/10.5281/zenodo.8077915">https://doi.org/10.5281/zenodo.8077915</a>, <a href="https://doi.org/10.5281/zenodo.6541983">https://doi.org/10.5281/zenodo.6541983</a></p> <p>The run output files are labeled using the following pattern: <code>hex-ca<capillary-number>-q<partial-charge>.tar.gz</code>. It is possible to obtain the wall speed/contact line speed from the capillary number using the following formula: <code>u_w = U_0*<capillary-number></code>, with <code>U_0 = 37.246 m/s</code>.</p> <p>To reproduce the runs it is necessary to use a specific version of Gromacs that allows for a special algorithm of pressure scaling with position restraints. The code can be obtained by cloning <a href="https://github.com/MicPellegrino/gromacs-flow-field.git">https://github.com/MicPellegrino/gromacs-flow-field.git</a>, and switching to the <code>flow-field-grid-visco-coms-deform</code> branch.</p> <p>The folder <code>conf-wat-hex.zip</code> contains the configuration files to reproduce MD simulations. To prepare the equilibration runs at constant pressure, run after having installed Gromacs:</p> <p><code>gmx grompp -f npt.mdp -p topology.top -c before-npt.gro -r before-npt.gro -o system-npt.tpr</code></p> <p>while to prepare the shear runs:</p> <p><code>gmx grompp -f shear.mdp -p topology.top -c after-npt.gro -r lambda0.gro -rb lambda1.gro -o system-shear.tpr</code></p> <p>Simulations are launched by running:</p> <p><code>gmx mdrun -v -s <tpr-file-name>.tpr <possibly-other-mdrun-flags></code></p> <p>Have fun simulating!</p>
Molecular simulations of nanoscale two-phase Couette flow of a water-hexane system on a hydrophilic substrate
<p>This dataset contains the output of Molecular Dynamics simulations (MD) of two-phase Couette flow of water/hexane biphasic systems, in terms of density, velocity and temperature fields. Instructions on how to read and analyze the output files in the <code>.tar.gz</code> archives can be found in these previously-published datasets: <a href="https://doi.org/10.5281/zenodo.8077915">https://doi.org/10.5281/zenodo.8077915</a>, <a href="https://doi.org/10.5281/zenodo.6541983">https://doi.org/10.5281/zenodo.6541983</a></p> <p>The run output files are labeled using the following pattern: <code>hex-ca<capillary-number>-q<partial-charge>.tar.gz</code>. It is possible to obtain the wall speed/contact line speed from the capillary number using the following formula: <code>u_w = U_0*<capillary-number></code>, with <code>U_0 = 37.246 m/s</code>.</p> <p>To reproduce the runs it is necessary to use a specific version of Gromacs that allows for a special algorithm of pressure scaling with position restraints. The code can be obtained by cloning <a href="https://github.com/MicPellegrino/gromacs-flow-field.git">https://github.com/MicPellegrino/gromacs-flow-field.git</a>, and switching to the <code>flow-field-grid-visco-coms-deform</code> branch.</p> <p>The folder <code>conf-wat-hex.zip</code> contains the configuration files to reproduce MD simulations. To prepare the equilibration runs at constant pressure, run after having installed Gromacs:</p> <p><code>gmx grompp -f npt.mdp -p topology.top -c before-npt.gro -r before-npt.gro -o system-npt.tpr</code></p> <p>while to prepare the shear runs:</p> <p><code>gmx grompp -f shear.mdp -p topology.top -c after-npt.gro -r lambda0.gro -rb lambda1.gro -o system-shear.tpr</code></p> <p>Simulations are launched by running:</p> <p><code>gmx mdrun -v -s <tpr-file-name>.tpr <possibly-other-mdrun-flags></code></p> <p>Have fun simulating!</p>
Molecular dynamics simulation of SpoIVFB:Pro-SigmaK complex (replicate 1)
<p>Replicate simulation 1/4</p> <p>Found here are all files needed to reproduce or visualize the results of molecular dynamics simulation of the SpoIVFB intramembrane protease bound to the transcription factor Pro-sigmaK. The protein complex was embedded in a POPE_POPG_DAG_CL bilayer using CHARMM-GUI and simulated using OpenMM. The README file is a C-shell script that will run equilibration and 250ns of unrestrained simulation. </p> <p>Individual output (.out) and trajectory (.dcd) files are provided for each checkpoint of the simulation. A combined trajectory containing 250 ns of unrestrained simulation is also provided (combined_250ns_traj.dcd). Together with the step5_input.psf file, this combined dcd file can be used with common software such as VMD to visualize the molecular dynamics trajectory.</p>
Molecular dynamics simulation trajectory of an anionic lipid bilayer: 100 mol% POPS with Na+ counterions using ff99 ions
<p><strong>System: </strong>Symmetric bilayer of anionic POPS (palmitoyl-oleoyl-phosphatidylserine 100 mol-%) lipids with sodium (Na<sup>+</sup>) counter ions.</p> <p><strong>Number of POPS:</strong> 128.<br> <strong>Number of Na<sup>+</sup>-ions:</strong> 128.<br> <strong>Number of waters:</strong> 4480.</p> <p><strong>Lipid model:</strong> Amber Lipid 17 [IR Gould, AA Skjevik, CJ Dickson, BD Madej, RC Walker: "Lipid17: A Comprehensive AMBER Force Field for the Simulation of Zwitterionic and Anionic Lipids" in prep. (2018)].</p> <p><strong>Ion model:</strong> Amber ff99 [J Åqvist <em>J. Phys. Chem.</em> <strong>94</strong> 8021 (1990)].</p> <p><strong>Water model:</strong> TIP3P [WL Jorgensen, J Chandrasekhar, JD Madura, RW Impey, ML Klein <em>J. Chem. Phys.</em> <strong>79</strong> 926 (1983)].</p> <p><strong>Simulation engine:</strong> Amber16 [DA Case et al. <em>AMBER 2017</em> UCSF (2017)].</p> <p><strong>Number of independent repeats per setup: </strong>2.<br> <strong>Trajectory lengths per repeat:</strong> 400 ns + 100 ns.<br> <strong>Previously equilibrated for:</strong> 100 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> 'Langevin' at T = 298 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984); <em>J. Chem. Phys.</em> <strong>103</strong> 10252 (1995)] with xy and z coupled separately at p = 1.0 bar with no surface tension.</p> <p><strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993);<em> J. Chem. Theory Comput.</em> <strong>9</strong> 3878 (2013)].<br> <strong>Van der Waals:</strong> Turned off between 1.0 nm and 1.5 nm.</p> <p><strong>Constraints: </strong>Lengths of covalent bonds involving Hydrogens in lipids using SHAKE [<em>J. Comput. Phys.</em> <strong>23</strong> 327 (1977)], in water using SETTLE [<em>J. Comput. Chem. </em><strong>13</strong> 952 (1992)].</p> <p><strong>Used in publications: </strong>OHS Ollila et al. "NMRlipids IV: Headgroup & glycerol backbone structures, and cation binding in bilayers with PS lipids" in prep (2018).</p>
Molecular dynamics simulation trajectory of an anionic lipid bilayer: 100 mol% DOPS with Na+ counterions using Joung-Cheetham Ions
<p><strong>System: </strong>Symmetric bilayer of anionic DOPS (1,2-Dioleoyl-<em>sn</em>-glycero-3-phosphoserine 100 mol-%) lipids with sodium (Na<sup>+</sup>) counter ions.</p> <p><strong>Number of DOPS:</strong> 128.<br> <strong>Number of Na<sup>+</sup>-ions:</strong> 128.<br> <strong>Number of waters:</strong> 4480.</p> <p><strong>Lipid model:</strong> Amber Lipid 17 [IR Gould, AA Skjevik, CJ Dickson, BD Madej, RC Walker: "Lipid17: A Comprehensive AMBER Force Field for the Simulation of Zwitterionic and Anionic Lipids" in prep. (2018)].</p> <p><strong>Ion models: </strong>Joung–Cheatham [IS Joung, TE Cheatham III <em>J. Phys. Chem. B </em><strong>112</strong> 9020 (2008)].</p> <p><strong>Water model:</strong> TIP3P [WL Jorgensen, J Chandrasekhar, JD Madura, RW Impey, ML Klein <em>J. Chem. Phys.</em> <strong>79</strong> 926 (1983)].</p> <p><strong>Simulation engine:</strong> Amber16 [DA Case et al. <em>AMBER 2017</em> UCSF (2017)].</p> <p><strong>Number of independent repeats per setup: </strong>2.<br> <strong>Trajectory lengths per repeat:</strong> 400 ns + 100 ns.<br> <strong>Previously equilibrated for:</strong> 100 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> 'Langevin' at T = 303 K.<br> <strong>Pressure coupling: '</strong>Berendsen' [<em>J. Chem. Phys.</em> <strong>81</strong> 3684 (1984); <em>J. Chem. Phys.</em> <strong>103</strong> 10252 (1995)] with xy and z coupled separately at p = 1.0 bar with no surface tension.</p> <p><strong>Electrostatics: </strong>PME [<em>J. Chem. Phys.</em> <strong>98</strong> 10089 (1993);<em> J. Chem. Theory Comput.</em> <strong>9</strong> 3878 (2013)].<br> <strong>Van der Waals:</strong> Turned off between 1.0 nm and 1.5 nm.</p> <p><strong>Constraints: </strong>Lengths of covalent bonds involving Hydrogens in lipids using SHAKE [<em>J. Comput. Phys.</em> <strong>23</strong> 327 (1977)], in water using SETTLE [<em>J. Comput. Chem. </em><strong>13</strong> 952 (1992)].</p> <p><strong>Used in publications: </strong>OHS Ollila et al. "NMRlipids IV: Headgroup & glycerol backbone structures, and cation binding in bilayers with PS lipids" in prep (2018).</p>
Assessment of mutation probabilities of KRAS G12 missense mutants and their long-time scale dynamics by atomistic molecular simulations and Markov state modeling: Datasets.
<p>Datasets related to the publication [1].<br> Including:</p> <ul> <li>KRAS G12X mutations derived from COSMIC v.79 [http://cancer.sanger.ac.uk/cosmic/] (KRAS_G12X_mut_COSMICv79..xlsx)</li> <li>RMSFs (300-2000ns) of GDP-systems (300_2000rmsf_GDP_systems_RAW_AVG_SE.xlsx)</li> <li>RMSFs (300-2000ns) of GTP-systems (300_2000RMSF_GTP_systems_RAW_AVG_SE.xlsx)</li> <li>PyInteraph analysis data for salt-bridges and hydrophobic clusters (.dat files for each system in the PyInteraph_data.zip-file)</li> <li>Backbone trajectories for each system (residues 4-164; frames for every 1ns). Last number (e.g. _1) refers to the replica of the simulated system.</li> <li>backbone_4-164.gro/.pdb/.tpr -files (resid 4-164) </li> </ul> <p><br> [1] Pantsar T et al. Assessment of mutation probabilities of KRAS G12 missense mutants and their long-time scale dynamics by atomistic molecular simulations and Markov state modeling. <em>PLoS Comput Biol Submitted</em> (2018)</p>
Molecular dynamics simulations of the interaction of the quadruple mutant human CYP2J2 (R111A + R117A + R382A + R446A) with arachidonic acid (POSES 1-3)
<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_quadmut_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of the quadruple R111A + R117A+R382A+R446A) mutant CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose). </p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p>
Molecular dynamics simulations of the interaction of mutant human CYP2J2 (R117A) with arachidonic acid (POSES 5-6)
<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_mutR117A_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of the R117A mutant CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose). </p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p> <p>005.md : Production stage</p> <p>006.analysis : Basic energy graphs</p> <p>007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)</p>
Molecular dynamics simulations of the interaction of wild type human CYP2J2 with DHA (POSES 1-4)
<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_wt_CYP2J2_DHA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of docosahexaenoic acid (DHA) in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 4 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose). </p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p> <p>005.md : Production stage</p> <p>006.analysis : Basic energy graphs</p> <p>007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)</p>
Molecular dynamics simulations of the interaction of wild type human CYP2J2 with arachidonic acid (POSES 3 and 4)
<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_wt_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 4 times, hence there are 4 repeats per pose). </p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p> <p>005.md : Production stage</p> <p>006.analysis : Basic energy graphs</p> <p>007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)</p>
Homology modelling, molecular docking and molecular dynamics simulations of wild type and mutant human CYP2J2 with three polyunsaturated fatty acids
<p>This is the "parent" repository for the Data Note : "­Molecular dynamics simulations of the interaction of wild type and mutant human CYP2J2 with polyunsaturated fatty acids" by Abelak, Bishop-Bailey and Nobeli.</p> <p>It contains a document (<strong>Abelak_etal_Methods.pdf</strong>) describing the methods used to produce the data here and the data in all repositories supplementing it.</p> <p>It also contains a shell script (<strong>create_sim4_repeats.sh</strong>) that is typical of those used to set up the molecular dynamics simulations in the repositories supplementing this one.</p> <p>Finally, it contains the results of the homology modelling and docking simulations that formed the starting points for the molecular dynamics simulations in this study.</p> <p>Description of files in this dataset:</p> <p><strong>C2J2_min3_mod_noH.pdb</strong> : Homology model of the wild type CYP2J2 built from an alignment of templates with PDB ids: 1SUO, 2P85, 3EBS and 1Z10.</p> <p><strong>docking_wild_type_C2J2.zip</strong> : Nine docked poses of arachidonic acid docked to the homology model of the wild type CYP2J2.</p> <p>Details of how this data was produced is available in the Abelak_etal_Methods.docx document.</p>
Molecular dynamics simulations of the interaction of wild type human CYP2J2 with arachidonic acid (POSES 1 and 2)
<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_wt_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 4 times, hence there are 4 repeats per pose). </p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p> <p>005.md : Production stage</p> <p>006.analysis : Basic energy graphs</p> <p>007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)</p>
Molecular dynamics simulations of the interaction of wild type human CYP2J2 with arachidonic acid (POSES 5 and 6)
<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_wt_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 4 times, hence there are 4 repeats per pose). </p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p> <p>005.md : Production stage</p> <p>006.analysis : Basic energy graphs</p> <p>007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)</p>
Molecular dynamics simulations of the interaction of the double mutant human CYP2J2 (R117A and R111A) with arachidonic acid (POSES 1-3)
<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_mutR111A_R117A_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of the double R111A + R117A mutant CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose). </p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p>
Molecular dynamics simulations of the interaction of mutant human CYP2J2 (R117A) with arachidonic acid (POSES 1-4)
<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_mutR117A_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of the R117A mutant CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose). </p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p> <p>005.md : Production stage</p> <p>006.analysis : Basic energy graphs</p> <p>007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)</p>
Molecular dynamics simulations of the interaction of mutant human CYP2J2 (R111A) with arachidonic acid (POSES 4-6)
<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_mutR111A_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of the R111A mutant CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose). </p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p> <p>005.md : Production stage</p> <p>006.analysis : Basic energy graphs</p> <p>007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)</p>
Molecular dynamics simulations of the interaction of wild type human CYP2J2 with EPA (POSES 1-4)
<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_wt_CYP2J2_EPA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of eicosapentaenoic acid (EPA) in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 4 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose). </p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p> <p>005.md : Production stage</p> <p>006.analysis : Basic energy graphs</p> <p>007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)</p>
Molecular dynamics simulations of the interaction of the quadruple mutant human CYP2J2 (R111A + R117A + R382A + R446A) with arachidonic acid (POSES 4-6)
<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_quadmut_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of the quadruple (R111A + R117A+R382A+R446A) mutant CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose). </p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p>
Evaluating Changes in the Local Protein Physicochemical En-vironment induced by Molecular Dynamics Simulation
<p><span>Mutation of a single amino acid residue may significantly affect the structure and function of an entire protein. The effect of single amino acid substitutions can be assessed by examining the physicochemical environment surrounding the amino acid of interest, an emerging form of quantification of which is multidimensional tensors. However, the effect with respect to a protein variant’s inherent dynamics in tensor space is rarely assessed despite the potential importance of this form of analysis in revealing local physicochemical properties of the protein and response to mutation. Using the wild-type and 936 mutant structures of the protein domain 1pga, the present research evaluated the effects of local protein context and single amino acid substitutions on molecular dynamics simulation-derived structural distributions via the use of tensors capturing a range of biochemical properties. It was observed that the extent of simulated </span><span>physicochemical</span><span> variation local to a substituted amino acid is positively associated with local mechanical stiffness, loss of protein thermostability and decreased local hydrophobicity. In addition, it was observed that the largest tensor variation occurs in densely-packed, hydrophobic core-associated regions of protein structures. In summary, the pattern of tensor change aligns with prior knowledge about protein stability and physicochemical properties.</span></p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.