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299 results for “MD simulation”
Dataset for protein docking and MD simulations of CARD-CARD interactions of the apoptosome
<p>Protein docking complexes and MD simulation trajectories for the Apaf1-Caspase9 CARD-CARD interactions and the cross-dockings between Apaf1 CARD and Caspase2 CARD, and RAIDD CARD and Caspase9 CARD, respectively (RAIDD and Caspase2 CARD domains interacting in the PIDDosome). Further details in the README file.</p>
Coevolution-driven constant pH MD Simulations of GPR68
<p>Contains all files necessary to reproduce the MD simulations and analysis, along with the CV generation pipeline for the paper "<span>Molecular basis of proton-sensing by G protein-coupled receptors</span>"</p> <p>The folder named "equilibration" contains all inputs and outputs generated during the equilibration phases, both with and without the cpH algorithm turned on.</p> <p>The folder named "AWH_inputs" contains all inputs necessary to replicate the work for pH6 and pH7 conditions, including parameters and the output pullx.xvg files plotted in SI fig 14.</p> <p>The folder named "CV_generation" contains all inputs and outputs generated during the CV generation procedure</p> <p>The "Titration_results" folder contains the output lambda coordinates for both pH6 and pH7, along with a decision plot showing why we honed in on a specific subset of titratable residues. </p> <p>Finally, the source code for GROMACS containing the merged versions of cpH and modern transformation pull coordinate and AWH code is contained in the "cpH_transformation_GROMACS" folder.</p> <p> </p>
Protein preparation (1LPB), docked structures of Bromhexine and Orlistat to Pancreatic Lipase, and MD simulations trajectories in 3 replicas.
<p>Data set contains 3 folders:</p> <p>1) Protein preparation (1LPB)</p> <p>2) XP Docking of Bromhexine and Orlistat</p> <p>3) MD Simulation of Bromhexine and Orlistat (3 replicates)</p>
Snapshots from MD simulations of bacterial and mitochondrial complex I
<p>These are the snapshots from classical MD simulations performed on complex I from <em>Thermus thermophilus</em> and <em>Bos taurus</em>. These files can be loaded into visualisation program VMD.</p>
The data about MD simulation
<p>The data about MD simulation support the findings of this study are openly available.</p>
Data for MD simulations (CSE)
<p>Data for Molecular Dynamics simulations of CSE, CSE+substrate, CSE+substrate+inhibitor at sites 12, 33 or 42.</p>
MD simulation trajectory of POPC/CHOL (18.75 mol%) bilayer and related files
<p>Simulation trajectory pre-equiblirated POPC/CHOL bilayer and related files from all-atom molecular dynamics simulations. The system contains 18.75mol% CHOL. Simulations have been performed with GROMACS-2021.2 with Lipid17 forcefield and TIP3P water model. The trajectory is 0-1000 ns, and we have disregarded the first 100 ns in our analysis.</p> <p>The system in the trajectory consists of 104 POPC, 24 CHOL and 6400 water molecules. Temperature 310 K, pressure 1 bar.</p> <p>Publication: <a href="https://doi.org/10.1016/j.bbamem.2022.183961">https://doi.org/10.1016/j.bbamem.2022.183961</a></p>
MD simulation trajectory of POPE bilayer and related files
<p>Simulation trajectory pre-equiblirated POPE bilayer and related files from all-atom molecular dynamics simulations. Simulations have been performed with GROMACS-2021.2 with Lipid17 forcefield and TIP3P water model. The trajectory is 0-1000 ns, and we have disregarded the first 100 ns in our analysis.</p> <p>The system in the trajectory consists of 128 POPE and 6400 water molecules. Temperature 310 K, pressure 1 bar.</p> <p>Publication: <a href="https://doi.org/10.1016/j.bbamem.2022.183961">https://doi.org/10.1016/j.bbamem.2022.183961</a></p>
MD simulation trajectory of SDPE bilayer and related files
<p>Simulation trajectory pre-equiblirated SDPE bilayer and related files from all-atom molecular dynamics simulations. Simulations have been performed with GROMACS-2021.2 with Lipid17 forcefield and TIP3P water model. The trajectory is 0-1000 ns, and we have disregarded the first 100 ns in our analysis.</p> <p>The system in the trajectory consists of 128 SDPE and 6400 water molecules. Temperature 310 K, pressure 1 bar.</p> <p>Publication: <a href="https://doi.org/10.1016/j.bbamem.2022.183961">https://doi.org/10.1016/j.bbamem.2022.183961</a></p>
MD simulation trajectory of POPC/DOG (18.75 mol%) bilayer and related files
<p>Simulation trajectory pre-equiblirated POPC/DOG bilayer and related files from all-atom molecular dynamics simulations. The system contains 18.75mol% DOG. Simulations have been performed with GROMACS-2021.2 with Lipid17 forcefield and TIP3P water model. The trajectory is 0-1000 ns, and we have disregarded the first 100 ns in our analysis.</p> <p>The system in the trajectory consists of 104 POPC, 24 DOG and 6400 water molecules. Temperature 310 K, pressure 1 bar.</p> <p>Publication: <a href="https://doi.org/10.1016/j.bbamem.2022.183961">https://doi.org/10.1016/j.bbamem.2022.183961</a></p>
MD simulation trajectory of POPE/CHOL (18.75 mol%) bilayer and related files
<p>Simulation trajectory pre-equiblirated POPE/CHOL bilayer and related files from all-atom molecular dynamics simulations. The system contains 18.75mol% CHOL. Simulations have been performed with GROMACS-2021.2 with Lipid17 forcefield and TIP3P water model. The trajectory is 0-1000 ns, and we have disregarded the first 100 ns in our analysis.</p> <p>The system in the trajectory consists of 104 POPE, 24 CHOL and 6400 water molecules. Temperature 310 K, pressure 1 bar.</p> <p>Publication: <a href="https://doi.org/10.1016/j.bbamem.2022.183961">https://doi.org/10.1016/j.bbamem.2022.183961</a></p>
MD simulation input files and results for ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"
<p>Input files and trajectories of n-alkane/lipid systems used in the article: ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids".</p> <p>Equilibrated starting configurations were created using CHARMM36. Otherwise, filenames specifiy the force field used (C36 or SL), Temperature and system composition.</p> <p>.xtc trajectories were created using gmx trjconv with options -pbc nojump -dt 10. run2 equals simulations from 100-200ns, run3 equals 200-300ns. The first 100ns were excluded from the analysis and are not included in this dataset.</p> <p>Exemplary .mdp files have been included for both force-fields. Please refer to the manuscript for the force field sources and additional information.</p>
MD simulations of FVa membrane binding 4/4
<p>For details see the publication:<br> "Understanding the complex membrane binding of a protein with multiple anchoring domains"<br> By J. J. Madsen & Y. Z. Ohkubo</p>
MD simulations of FVa membrane binding 3/4
<p>For details see the publication:<br> "Understanding the complex membrane binding of a protein with multiple anchoring domains"<br> By J. J. Madsen & Y. Z. Ohkubo</p>
MD simulations of FVa membrane binding 1/4
<p>For details see the publication:<br> "Understanding the complex membrane binding of a protein with multiple anchoring domains"<br> By J. J. Madsen & Y. Z. Ohkubo</p>
MD simulations of FVa membrane binding 2/4
<p>For details see the publication:<br> "Understanding the complex membrane binding of a protein with multiple anchoring domains"<br> By J. J. Madsen & Y. Z. Ohkubo</p>
Pure POPC bilayer MD simulations with CHARMM36 force field with GROMACS_v2019
<p>500 ns MD simulation of POPC bilayer with CHARMM36 force field at 300 K generated with GROMACS 2019 simulation engine. The system contains 100 POPC lipids per leaflet (200 in total) and 2000 TIP3P water molecules. No, NaCl in the system. This data set contains 500 ns data with 50000 frames (saving frequency is every 10 ps). </p>
MD Simulations of a1b2g2 GABA-A receptor
<p>MD simulations in Shared structural mechanisms of general anaesthetics and benzodiazepines</p> <p>DOI: 10.1038/s41586-020-2654-5</p>
Initial and final MD simulation coordinates for "Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization"
<p>Initial and final coordinates for all MD simulations performed for the manuscript: "Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization."</p> <p>File uploaded is a ZIP folder, containing sub-folders for each capsid construct (wild type and mutants). Additionally, a README file is given in the top-level folder, which contains a description of the file contents.</p>
MD_Simulations_Molecular_mechanisms_of_inorganic-phosphate_release_from_the_core_and_barbed_end_of_actin_filaments
<p>This repository contains the models, protocols, datasets and Jupyter notebooks to reproduce the computational experiments in the paper:</p> <p>"Molecular mechanisms of inorganic-phosphate release from the core and<br> barbed end of actin filaments"</p> <p>by W. Oosterheert, F.E.C Blanc, A. Roy, A. Belyy, M.B. Sanders,, O. Hofnagel, G. Hummer, P. Bieling, S. Raunser</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.