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Dataset results
691 results for “Molecular dynamics”
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>
Example dataset for openPMD-conform molecular dynamics data (MD domain extension)
<p>This dataset results from the molecular dynamics (MD) simulation of the photon-sample interaction. The photons are propagated through the SASE1 beamline and the SPB-SFX instrument at European XFEL, with an initial energy of 5 keV. The sample is the two-nitrogenase iron protein (2nip) with 4348 atoms. The simulation is performed with a demo version of XMDYN. The datasets were rewritten from the original XMDYN output into an hdf5 format that complies with the openPMD metadata standard for particle and mesh data and the proposed domain extension of this standard for MD data. The dataset "pure_2nip_pmi_out.opmd.h5" conforms the openPMD metadata MD domain extension strictly, while the dataset "pure_2nip_pmi_out.opmd.ff.h5" stores form factor results additionally for SingFEL diffraction simulation.</p> <p>This dataset is part of the Deliverable D5.1 in Workpackage 5 (Virtual Neutron and X-ray Laboratory) of the Photon and Neutron Open Science Cloud (PaNOSC).</p> <p>This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 823852.<br> </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>
'Invisible' Molecular Dynamics Revealed for a Conformationally Chiral π-Stacked Perylene Bisimide Foldamer
<p>Additional data to report <a href="https://doi.org/10.1002/anie.202414069">https://doi.org/10.1002/anie.202414069</a>:</p> <p><a name="_Hlk172654864"></a>Whilst energetic and kinetic aspects of folding processes are meanwhile well understood for natural biomacromolecules, the folding dynamics in so far studied artificial foldamer counterparts remain largely unexplored. This is due to the low energy barriers between their conformational isomers that make the dynamic processes undetectable with conventional methods such as UV/vis absorption, fluorescence, and NMR spectroscopy, making such processes ‘invisible’. Here we present an asymmetric perylene bisimide dimer (bis-PBI <strong>1</strong>) that possesses conformational chirality in its folded state. Owing to the large interconversion barrier (≥ 116 kJ mol<sup>–1</sup>), four stereoisomers could be separated and isolated. Since the interconversion between these stereoisomers requires the foldamer to first open and then to re-fold, the transformation of one stereoisomer into others allowed us to ‘visualize’ the dynamics of folding with time and determine its lifetimes and the energetic barriers associated with the folding process. Supported by quantum chemical calculations, we identified the open structure to be only a fleeting metastable state of higher energy. Our experimental observation of the kinetics associated with the molecular dynamics in the PBI foldamer advances the fundamental understanding of folding in synthetic foldamers and paves the way for the design of smart functional materials.</p>
Molecular Dynamics Simulation of SARS-CoV-2 Spike Protein
<p>Trajectory data corresponding to the manuscript, tentatively titled "Distant Residues Modulate the Conformational Opening in SARS-CoV-2 Spike Protein"</p> <p>Authors: Dhiman Ray, Ly Le, Ioan Andricioaei</p> <p>Affiliation: University of California Irvine, USA</p> <p>Description: Multiple unbiased simulations of 40 ns were performed for the SARS-CoV-2 spike protein. Frames are saved at 50 ps interval. The initial structures were generated from umbrella sampling simulation starting from PDB ID: 6VSB and 6VXX. The index at the end of filename stands for the umbrella sampling window from which the trajectory was initiated. The indices are not continuous as not all the umbrella sampling windows were used to start trajectories. Additionally 3 trajectories, each of length 80 ns, are included for the closed, partially open and fully open state. The topology is provided as a PDB file ("spike_dry.pdb").</p> <p>The trajectories are for the spike head only structure obtained from the CHARMM-GUI Covid-19 archive. No solvent or ions are included in the trajectory or the topology.</p> <p>Update: Additional trajectories and PDB files for D614G mutant added. Each trajectory is 40 ns long. The PDB files are named 6VXX_mutant_dry.pdb and 6VSB_mutant_dry.pdb for the closed and partially open state.</p> <p>Pre-print available: https://doi.org/10.1101/2020.12.07.415596</p>
Mutually Beneficial Combination of Molecular Dynamics Computer Simulations and Scattering Experiments - DATA
<p>Specular reflectivities of the SoyPC bilayer stack measured at the vertical reflectometer MARIA at Heinz Maier-Leibnitz Zentrum (MLZ) in Garching, Germany.</p> <p>Offspecular reflectivity map (log scale) of the multilayer sample as a function of theangle of incidence (θi) and of the reflection angle (θi).</p> <p>Specular reflectivities of the Si/SiO<sub>2</sub>/DMPC/H2O at 4 different contrasts (H<sub>2</sub>O, D<sub>2</sub>O, SMW and 4MW)</p> <p>Small-angle neutron scattering of the unilamellar SoyPC</p>
Coarse-grained molecular dynamics simulations of SARS-CoV-2 envelope protein E in the pentameric form
<p>The trajectories of coarse-grained (CG) molecular dynamics (MD) simulations of<br> 1) unmodified (FeigLab_NMR; FeigLab_PentamerNoPTM_POPC_Martini3b: 5 μs; 5 μs); <br> 2) palmitoylated (FeigLab_PentamerCYSP43; PentamerCYSP44_POPC_Martini3b: 5 μs; 5 μs); <br> SARS-CoV-2 E protein pentamer in a POPC bilayer.</p> <p>The trajectory of CG MD of system containing 2 pentamers in the membrane buckled in a single direction (BuckledMembrane_FeigLab_2xPentamerNoPTM_POPC_Martini3b: 1 μs).</p> <p>FeigLab_Pentamer: https://github.com/feiglab/sars-cov-2-proteins/blob/master/Membrane/E_protein.pdb<br> FeigLab_NMR_Pentamer is assembled based on the transmembrane domain determined by NMR (PDB ID: 7K3G) and FeigLab model for the rest.</p>
Molecular dynamics of ALDH1/2
<p>Members of the aldehyde dehydrogenase (ALDHs) superfamily have unique characteristics at their substrate binding site, where they catalyze the NAD+-dependent oxidation of aldehydes to their respective carboxylic acids. Molecular dynamics simulations, performed with the GROMACS 2022 package, have investigated the dynamics of the substrate binding site, using ALDH1 (PDB ID: 6B5G) and ALDH2 (PDB ID: 5L13) crystallographic structures. The tetrameric structures were simulated for 100 ns in: (1) APO (without any ligand bounded) state; (2) NAD-bounded state; (3) subtrate-bounded state; and (4) NAD- and substrate-bounded state. A total of 101 frames were extracted at regular intervals of 100 ps from the molecular dynamics trajectory. The ligands were removed from the substrate binding site after production to ease analysis.</p>
Research data supporting: "Unsupervised Data-Driven Reconstruction of Molecular Motifs in Simple to Complex Dynamic Micelles"
<p>This repository contains the set of data shown in the paper <strong>"Unsupervised Data-Driven Reconstruction of Molecular Motifs in Simple to Complex Dynamic Micelles"</strong>, published on The Journal of Physical Chemistry B (DOI:10.1021/acs.jpcb.2c08726).</p>
Binding site plasticity regulation of the FimH catch-bond mechanism: Molecular Dynamics dataset
<p>Dataset of Molecular Dynamics simulations and analysis scripts used in the article "Binding site plasticity regulation of the FimH catch-bond mechanism" [<a href="https://doi.org/10.1016/j.bpj.2023.05.029">paper</a>][<a href="https://doi.org/10.1101/2022.11.15.516604">bioRxiv</a>].</p> <p>Contains:</p> <ul> <li>Replica Exchange with Solute Scaling (REST2) simulations of the FimH protein lectin domain in its two main allosteric states (Associated and Separated), in presence and absence of its synthetic ligand heptyl α-ᴅ-mannose (input files and trajectories of the unscaled replicas)</li> <li>Replica Exchange Umbrella Sampling (REUS) simulations of the liganted systems along a collective variable (CV) describing binding site opening (input files and trajectories)</li> <li>REUS simulations in presence of a pulling force on the protein-ligand complex.</li> </ul> <p>See the article for more details.</p>
Molecular dynamics trajectories for "Reservoir-REMD facilitates kinetic rescue from metastable peptide conformations
<p>The molecular dynamics-generated ensemble dataset for cyclo-(cGHHQKLV), used in the manuscript "Reservoir-REMD facilitates kinetic rescue from metastable peptide conformations". The dataset consists of 14 + 6 =20 .dcd files, and one .pdb file for rendering.</p>
Dataset of Molecular Dynamics Simulations for the Upregulated Biomarker PSMB8: 3UNF and its G210V Mutant in Experimental Autoimmune Encephalomyelitis
<p>This dataset contains molecular dynamics simulations data generated using GROMACS for the upregulated biomarker 3UNF and its G210V mutant in the context of Experimental Autoimmune Encephalomyelitis (EAE). EAE is a widely studied animal model for multiple sclerosis, and investigating the behavior of biomarkers in this model is crucial for understanding disease progression and potential therapeutic interventions.</p> <p>The dataset includes trajectory files, coordinate files, and relevant parameters used in the simulations. These simulations provide valuable insights into the structural dynamics, conformational changes, and interactions of the PSMB8 biomarker 3UNF and its G210V mutant within the EAE system. The data offers researchers an opportunity to analyze and explore the behavior of these biomarkers at the atomic level, aiding in the identification of potential binding partners, functional sites, and mechanisms associated with disease progression.</p> <p>By sharing this dataset, we aim to contribute to the scientific community by providing a valuable resource for further analysis, validation, and comparison of the molecular behavior of the upregulated biomarker 3UNF and its G210V mutant in Experimental Autoimmune Encephalomyelitis.</p>
Molecular dynamics simulation data 1: Structure of the connexin-43 gap junction channel in a putative closed state
<p>Molecular dynamics data for the manuscript Qi C.*, Acosta-Gutierrez S.*, Lavriha P., Othman A., Lopez-Pigozzi D., Bayraktar E., Schuster D., Picotti P., Zamboni N., Bortolozzi M., Gervasio F.L., Korkhov V.M. Structure of the connexin-43 gap junction channel in a putative closed state. eLife (2023) <a href="https://doi.org/10.7554/eLife.87616.2">https://doi.org/10.7554/eLife.87616.2</a></p> <p>The dataset includes:</p> <p>1. The starting coordinates, topology, MD inputs</p> <p>2. Production run gromacs trajectories for the Cx43 gap junction channel</p>
Molecular dynamics simulation based analysis of celecoxib-polymer interactions
<p>This dataset contains scripts and coordinate files for running and analysing molecular dynamics simulations to investigate celecoxib-polymer interactions in aqueous solution. Trajectory files (stripped of water and ions) are included.</p> <p>The associated study is described in:</p> <p>" Comparative analysis of drug-salt-polymer interactions by experiment and molecular simulation improves biopharmaceutical performance", Sumit Mukesh, Goutam Mukherjee, Ridhima Singh, Nathan Steenbuck, Carolina Demidova, Prachi Joshi, Abhay T. Sangamwar, Rebecca C. Wade, submitted.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.