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Dataset results
15 results for “CYP2J2”
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>
Molecular dynamics simulations of the interaction of mutant human CYP2J2 (R111A) with arachidonic acid (POSES 1-3)
<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 the double mutant human CYP2J2 (R117A and R111A) with arachidonic acid (POSES 4-6)
<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>
CYP2J2 Modulates Diverse Transcriptional Programs in Adult Human Cardiomyocytes
GEO Series GSE136957. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
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