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691 results for “Molecular dynamics”
Data for: Optimal inference of molecular interaction dynamics in FRET microscopy
<p>Intensity-based time-lapse fluorescence resonance energy transfer (FRET) microscopy has been a major tool for investigating cellular processes, converting otherwise unobservable molecular interactions into fluorescence time series. However, inferring the molecular interaction dynamics from the observables remains a challenging inverse problem, particularly when measurement noise and photobleaching are nonnegligible—a common situation in single-cell analysis. The conventional approach is to process the time-series data algebraically, but such methods inevitably accumulate the measurement noise and reduce the signal-to-noise ratio (SNR), limiting the scope of FRET microscopy. Here, we introduce an alternative probabilistic approach, B-FRET, generally applicable to standard 3-cube FRET-imaging data. Based on filtering theory, B-FRET implements a statistically optimal way to infer molecular interactions and thus drastically improves the SNR. We validate B-FRET using simulated data and then apply it to real data, including the notoriously noisy in vivo FRET time series from individual bacterial cells to reveal signaling dynamics otherwise hidden in the noise.</p>
Molecular dynamics-generated ensemble dataset of ubiquitin; for "PROTHON: A Local Order Parameter-Based Method for Efficient Comparison of Protein Ensembles"
<p>The molecular dynamics-generated ensemble dataset (229Mb zip file) for ubiquitin, used in the manuscript "PROTHON: A Local Order Parameter-Based Method for Efficient Comparison of Protein Ensembles", submitted to the Journal of Chemical Information and Modeling (JCIM). The dataset consists of 6 .dcd files, and one .pdb file. </p>
Molecular dynamics (MD) simulations methods and results on cyclooctene oxides in ACN/water hybrid electrolytes
<p><strong>Molecular dynamics (MD) simulations methods and extended results used for the <em>Perspective</em> article entitled</strong></p> <p>“Fine tuning of electrosynthesis pathways by modulation of electrolyte solvation structure”</p>
Molecular Simulation Data Associated with the Manuscript "Function and dynamics of the intrinsically disordered carboxyl terminus of β2 adrenergic receptor"
<p>Molecular Simulation Data Associated with the Manuscript<br> <br> "Function and dynamics of the intrinsically disordered carboxyl terminus of β2 adrenergic receptor"<br> <br> by Jie Heng, Yunfei Hu, Guillermo Pérez-Hernández, Asuka Inoue, Jiawei Zhao, Xiuyan Ma, Xiaoou Sun, Kouki Kawakami, Tatsuya Ikuta, Jienv Ding, Yujie Yang, Lujia Zhang, Sijia Peng, Xiaogang Niu, Hongwei Li, Ramon Guixà-González, Changwen Jin, Peter W. Hildebrand, Chunlai Chen & Brian K. Kobilka</p> <p>Nature Communications 2023, <a href="https://doi.org/10.1038/s41467-023-37233-1">https://doi.org/10.1038/s41467-023-37233-1</a><br> <br> The representative molecular dynamics (MD) trajectories shown in the <strong>Supplementary Fig. 8,<br> Variable contacts of the β2AR CT</strong> can be 3D visualized in the browser in the following link:</p> <ul> <li><a href="https://proteinformatics.uni-leipzig.de/mdsrv.html?load=file://base/B2CT/variants.ngl"> https://proteinformatics.uni-leipzig.de/mdsrv.html?load=file://base/B2CT/variants.ngl</a></li> </ul>
EMD data for the paper "Impact of ad-hoc post-processing parameters on the lubricant viscosity calculated with equilibrium molecular dynamics simulations"
<p>This archive contains the post-processing data obtained from EMD simulations of <strong>2,2,4-Trimethylhexane</strong> lubricant molecule under various operating conditions. The EMD simulations were performed using LAMMPS with COMPASS force field. (See manuscript and README for details.)</p>
Protein Structure Files and Galaxy Workflows for Conducting Molecular Dynamics Simulations of Flavivirus Helicases -- Output Files
<p>These are the output files generated using the input files and Galaxy workflows for flavivirus helicase simulations, from: </p> <pre>https://doi.org/10.5281/zenodo.7493015</pre>
Molecular dynamics trajectories of MTDH-SND1 protein-protein interaction inhibitors
<p>This includes the prmtop and MD trajectories (production stage) and Amber outfiles of L1-L12, C26-A6/2, and MTDH peptide, GaMD trajectories of the protein, and the umbrella sampling trajectories of L5 and C26-A6/2. To reduce the file size, the trajectory files had been compressed using “xz” algorithm, and frames were saved by one frame per 1ns. However, for reference, one additional larger traj file with higher saving frequency for L5 was also uploaded. The input files and input coordinate files were uploaded as a separate attachment at http://pubs.acs.org.</p>
Molecular Dynamics Trajectory of CsPbI3 produced using ACE MLFF
<p>Molecular dynamics trajectories of CsPbI3, with 2 fs timestep between computed frames, frames are recorded every 200 fs. Under each folder, there are three npz files (each contains 100 ps of trajectory) and one initial configuration LAMMPS data file. The npz files can be read with 'numpy.load'. There are three entries for each npz object, 'positions' for the atomic positions, 'cells' for the lattice dimensions, and 'numbers' for the atomic number of the species. </p>
Molecular Dynamics Trajectory of CH3NH3PbBr3 produced using VASP MLFF
<p>Molecular dynamics trajectories of CH3NH3PbBr3, with 1 fs timestep between computed frames, frames are recorded every 50 fs. </p>
Data supporting Mixed-anion mixed-cation perovskite (FAPbI3)0.875(MAPbBr3)0.125: an ab initio molecular dynamics study
<p>Data of a molecular dynamics simulation of the mixed cation and mixed halide perovskite (FAPbI3)0.875(MAPbBr3)0.125 , as well as the end compounds FAPbI3 and MAPbBr3.</p> <p>Related article: </p> <p><em><strong>J. Mater. Chem. A</strong></em>, 2022,<strong>10</strong>, 9592-9603, <a href="https://doi.org/10.1039/D1TA10860C">https://doi.org/10.1039/D1TA10860C</a></p> <p>arXiv:2112.09795 [cond-mat.mtrl-sci] arXiv: 2112.09795 <a href="https://doi.org/10.48550/arXiv.2112.09795">https://doi.org/10.48550/arXiv.2112.09795</a></p>
Molecular dynamics simulation input files: Histone Tail Electrostatics Modulate E2-E3 Enzyme Dynamics: A Gateway to Regulate Ubiquitination Machinery
<p>Molecular dynamics simulation input files: Histone Tail Electrostatics Modulate E2-E3 Enzyme Dynamics: A Gateway to Regulate Ubiquitination Machinery (<a href="https://zenodo.org/record/7423328">https://zenodo.org/record/7423328</a>)</p>
Molecular dynamics simulations of CD59 and CD59-inhibited Membrane Attack Complex
<p>Coarse-grain (CG) trajectories of CD59-C5b8 (last 1,500 ns):</p> <ul> <li>cd59-c5b8_1500ns_rep1.xtc</li> <li>cd59-c5b8_1500ns_rep2.xtc</li> <li>cd59-c5b8_1500ns_rep3.xtc</li> </ul> <p>PyLipID analysis results from CG CD59-C5b8 simulations:</p> <ul> <li>Interactions_CHOL.csv</li> <li>Interactions_DOPC.csv</li> </ul> <p>Atomistic CD59 simulations in DOPC membrane:</p> <ul> <li>cd59_at_rep1_light.trr</li> <li>cd59_at_rep2_light.trr</li> <li>cd59_at_rep3_light.trr</li> </ul> <p>CD59 Euler angles relative to the membrane: </p> <ul> <li>rep1.csv</li> <li>rep2.csv</li> <li>rep3.csv</li> </ul> <p>All xtc and trr files were down-sampled (frames removed) to decrease file size.</p>
Equilibrium Molecular Dynamics of aqueous glycerol menisca
<p>This dataset contains the results of Molecular Dynamics simulations of quasi-2D water-glycerol liquid meniscus, confined between silica-like surfaces. The goal of the simulations is to observe and quantify liquid density layering close to solid surfaces.</p> <p>The pattern "Glycerol***" refers to the mass fraction of glycerol ("000": pure water, "100": pure glycerol). Each folder contains configuration files and compressed output molecular trajectories. Post-processing is performed on density maps binned on-the-fly using a customized Gromacs version (<a href="https://github.com/pjohansson/gromacs-flow-field">https://github.com/pjohansson/gromacs-flow-field</a>); frames are placed in a tarball ("wat-gly-*p-eq.tar.gz").</p> <p>The zipped folder 'scripts.zip' contains a self-contained library of functions to read density maps and a Jupyter notebook with an example of density reading and plotting.</p> <p>Simulations are performed with Gromacs. We refer to the code documentation for further information (<a href="https://manual.gromacs.org/">https://manual.gromacs.org/</a>).</p>
AutoParams: An Automated Web-Based Tool To Generate Parameters for Molecular Dynamics Simulations
<p>Dataset of thirteen (13) compounds used to test the AutoParams webserver. Includes initial PDB files, generated parameters (mol2/frcmod files), and resulting AMBER-formatted MD inputs (prmtop/inpcrd). Additionally, includes 2D structure in PNG format and canonical SMILES string in .smi file format.</p>
Supporting data for:"An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations."
<p>PLUMED_NEST_REPO.zip contains the plumed.dat file and the template PDB used to perform the metainference MD simulations of Gelsolin and UP1-RNA, with and without the Solvation Layer Contribution.</p> <p>TRAJECTORIES.zip contains the Gelsolin and UP1-RNA trajectories and additional data generated with GROMACS. In details:</p> <p>-Gelsolin. Production Molecular Dynamics Parameter file (production.mdp), a topology file (topol.top), and 3 folders: TPRs (with 10 TPR files -one for each replica-), TRJ_SLC_OFF (with data from simulations without Solvation Layer Contribution), and TRJ_SLC_ON (with data from simulations with Solvation Layer Contribution). The last two contain an index file, a trajectory obtained from the concatenation of the 10 replicas (concat.xtc), and a template PDB file.</p> <p>-UP1-RNA. TPR file (md.tpr) and 2 folders: TRJ_SLC_OFF (with data from simulations without solvent correction), and TRJ_SLC_ON (with data from simulations with solvent correction). Each folder contains an index file, a template PDB file and a trajectory file (trj.xtc)</p> <p> </p>
Identification of Potential JNK3 Inhibitors Through Virtual Screening, Molecular Docking And Molecular Dynamics Simulation as Therapeutics for Alzheimer's Disease
<p>Alzheimer's disease (AD) is a complex neurological disorder without effective treatment. One factor in its development is c-Jun N-terminal kinases (JNKs), a type of protein related to brain function. JNK3, found mainly in the brain, contributes to AD by promoting brain abnormalities. Current research aims to create new JNK3 inhibitors for AD treatment using a virtual screening method. A database of compounds was filtered, and five potential compounds were identified with better scores than a reference. These compounds underwent simulations and energy calculations, showing stability and potential as JNK3 inhibitors.</p>
Molecular dynamics simulation trajectories for the GB99dms implicit solvent force field
<p>Molecular dynamics simulation trajectories used in training and validating the GB99dms implicit solvent protein force field. See the paper:</p> <ul> <li>Greener JG. Differentiable simulation to develop molecular dynamics force fields for disordered proteins, <a href="https://doi.org/10.1039/D3SC05230C" target="_blank" rel="noopener">Chemical Science</a> 15, 4897-4909 (2024)</li> </ul> <p>For more information, including structure files for these trajectories, see https://github.com/greener-group/GB99dms.</p>
Molecular dynamics simulations of hyaluronan octamer–tetrapeptide mixtures
<p><strong>To cite:</strong> Riopedre-Fernandez, M.; Biriukov, D.; Dračínský, M.; Martinez-Seara, H. Hyaluronan-arginine enhanced and dynamic interaction emerges from distinctive molecular signature due to electrostatics and side-chain specificity. Carbohydr. Polym. 2024, 325, 121568. DOI: <a href="https://doi.org/10.1016/j.carbpol.2023.121568">10.1016/j.carbpol.2023.121568</a></p> <p>MD simulations of hyaluronan octamer (HA8) with tetrapeptides. Simulation files and molecular topologies are provided.</p> <p>Tetrapeptides simulated: tetraarginine (R4), tetralysine (K4), tetraalanine (A4), tetraproline (P4), tetraglycine (G4), arginine-lysine-arginine-lysine (RKRK), and tetraglutamic acid (E4).</p> <p>Two force fields were compared: CHARMM (version charmm36-jul2020.ff.tgz from <a href="http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs">http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs</a>) and prosECCo75 (<a href="https://gitlab.com/sparkly/prosecco/prosECCo75">https://gitlab.com/sparkly/prosecco/prosECCo75</a>).</p> <p>Each simulation contained one hyaluronan polymer, one tetrapeptide, CHARMM-specific TIP3P water, and potassium counterions (standard "K" model in CHARMM and "K_s" model in prosECCo75) when necessary.</p> <p>We also additionally performed: (i) reference simulations with only hyaluronan octamer and potassium counterions; (ii) reference simulations with only R4 or K4 peptide and chloride counterions; (iii) simulations with two peptides (R4, K4, or G4) and two hyaluronan octamers.</p> <p>Simulations were done in Gromacs.</p> <p>Length - at least 1 µs, prolonged till 2 µs for prosECCo75 systems with R4, K4, or G4 peptides.</p> <p>Temperature - 300 K.</p> <p>For peer-reviewing process, extracted PDB configurations (a configuration every 10 ns of 2 μs simulations excluding the first 100 ns of equilibration) from selected systems were separately uploaded to <a href="http://doi.org/10.5281/zenodo.8423276">http://doi.org/10.5281/zenodo.8423276</a></p>
Introduction to HPC: molecular dynamics simulations with GROMACS: log files
<p>Introduction to HPC: molecular dynamics simulations with GROMACS: log files corresponding to the exercises 1.X 2.X 3.X</p>
Molecular dynamics simulations of hyaluronan octamer–tetrapeptide mixtures (PDB configurations)
<p>Extracted PDB configurations from MD simulations of hyaluronan octamer (HA8) with R4 and K4 tetrapeptides. Simulated explicit water was removed for clarity.</p> <p>See <a href="https://doi.org/10.5281/zenodo.8028600">10.5281/zenodo.8028600</a> for more details about simulated systems.</p>
ScienceDex guides
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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.