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691 results for “Molecular dynamics”
AlphaFold2 Modeling and Molecular Dynamics Simulations of the Conformational Ensembles for the SARS-CoV-2 Spike Omicron JN.1, KP.2 and KP.3 Variants : Mutational Profiling of Binding Energetics Reveals Epistatic Drivers of the ACE2 Affinity and Escape Hotspots of Antibody Resistance
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Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study- PART 6
<p>Trajectories and input files of the simulations of the S151T Rbfox*·pre-miR20b* system.</p>
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study- PART 1
<p>Simulations of the Rbfox protein.</p> <p> </p>
Dataset for molecular dynamics simulations of coalescence of Pd and AuPd clusters
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Molecular dynamics simulation trajectories of homorepeat peptides
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Molecular dynamic trajectories for PLGF and VEGF complexed with custom designed aptamers
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Comparative structural insights and functional analysis for the distinct unbound states of Human AGO proteins - Molecular dynamics trajectories and analysis scripts
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Molecular dynamics of the PS4Ab1
<p>Molecular dynamics of the PS4Ab1 protein using 100-ns long MD simulations.</p>
Molecular Dynamics Trajectories for GPR6 with Ligand IAG (Inverse Agonist)
<p>Molecular Dynamics Data for 10.1126/scisignal.ado8741 for publication at</p> <p>Barekatain M., Johansson L.C., Lam J.H. et al Structural Insights into the High Basal Activity and Inverse Agonism of the Orphan Receptor GPR6 Implicated in Parkinson's Disease, Sci Signal. 2024 Dec 3;17(865):eado8741. doi: 10.1126/scisignal.ado8741. Epub 2024 Dec 3.</p> <p>This folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.1 ns per frame. Periodic boundary condition (pbc) can be restored using VMD's standard pbc commands.</p> <p>Please cite us if you find this data useful!</p>
Suppl Material- Pharmacokinetics of some newly synthesized 1, 5- benzothiazepine scaffolds: A molecular docking and molecular dynamics simulation approach
<p>It is suppl material, table and figures for publications</p>
Simulation trajectories from ab-initio molecular dynamics of 4x4x4 super cell of Li3OCl with 4 Li concentrations
<p>Lithium-rich oxychloride antiperovskites are promising solid electrolytes for enabling next-generation batteries. Here, we report a comprehensive study varying Li<sup>+</sup> concentrations in Li<sub>3</sub>OCl using <em>ab-initio</em> molecular dynamics simulations. The simulations accurately capture the complex interactions between Li<sup>+</sup> vacancies (V'<sub>Li</sub>), the dominant mobile species in Li<sub>3</sub>OCl. The V'<sub>Li</sub> polarize and distort the host lattice, inducing additional non-vacancy mediated diffusion mechanisms and correlated diffusion events that reduce the activation energy barrier at concentrations as low as 1.5% V'<sub>Li</sub>. Our analyses of discretized diffusion events Li in both space and time illustrate the critical interplay between correlated dynamics, polarization, and local distortion in promoting ionic conductivity in Li<sub>3</sub>OCl.</p>
Controlled coherent dynamics of [VO(TPP)], a prototype molecular nuclear qudit with an electronic ancilla. Open data set
<p>Data supporting the original figures 2, 3, 4, 5, 6, 7, 8 of the related publication.</p>
data for "An unbound proline-rich signaling peptide frequently samples cis conformations in Gaussian accelerated molecular dynamics simulations"
<p>Disordered proline-rich motifs are common across the proteomes of many species and are often involved in protein-protein interactions. Proline is a unique amino acid due to the covalent bond between the backbone nitrogen and the proline side chain. The resulting five-membered ring allows proline to sample the <em>cis</em> state about its peptide bond, which other residues cannot do as readily. Because proline-rich disordered sequences exist as ensembles that likely include structures with the proline peptide bond in <em>cis</em>, a robust methodology to accurately account for these conformations in the overall ensemble is crucial. Observing the <em>cis </em>conformations of proline in a disordered sequence is challenging both experimentally and computationally. Nitrogen-hydrogen NMR spectroscopy cannot directly observe proline residues, which lack an amide bond, and computational methods struggle to overcome the large kinetic barrier between the <em>cis </em>and <em>trans </em>states, since isomerization usually occurs on the order of seconds. In the current work, Gaussian accelerated molecular dynamics was used to overcome this free energy barrier and simulate proline isomerization in a tetrapeptide (KPTP) and in the 12-residue proline-rich SH3 binding peptide, ArkA. We found that Gaussian accelerated molecular dynamics, when combined with a lowered peptide bond dihedral angle potential energy barrier (15 kcal/mol), allowed sufficient sampling of the proline <em>cis </em>and <em>trans </em>states on a microsecond timescale. All ArkA prolines spend a significant fraction of time in <em>cis</em>, leading to a more compact ensemble with less polyproline II helix structure than an ArkA ensemble with all peptide bonds in <em>trans</em>. The ensemble containing <em>cis</em> prolines also matches more closely to <em>in vitro</em> circular dichroism data than the all-<em>trans</em> ensemble. The ability of the ArkA prolines to isomerize likely affects the peptide’s ability to bind its partner SH3 domain, and should be studied further. This is the first molecular dynamics simulation study of proline isomerization in a biologically relevant proline-rich sequence that we know of, and a similar protocol could be applied to study multi-proline isomerization in other proline-containing proteins to improve conformational diversity and agreement with <em>in vitro</em> data.</p>
Molecular dynamics simulations of BmrA starting from X-ray and cryo-EM structure
<p>This archive contains all the MD trajectories presented in the article<br> 'Drug-bound and -free outward-facing structures of a multidrug ABC exporter point to a swing mechanism'<br> by Chaptal et al,<br> https://doi.org/10.1101/2021.03.12.435132</p> <p><br> MD simulations of the BMRA Xray structure:<br> - 4 replicates with short equilibration:<br> BMRA_Xray_run1<br> BMRA_Xray_run2<br> BMRA_Xray_run3<br> BMRA_Xray_run4 <br> - 2 replicates with long equilibration:<br> BMRA_Xray_run5<br> BMRA_Xray_run6</p> <p>MD simulations of the BMRA Cryo-EM:<br> - 4 replicates with short equilibration:<br> BMRA_Cryo_run1<br> BMRA_Cryo_run2<br> BMRA_Cryo_run3<br> BMRA_Cryo_run4<br> - 2 replicates with long equilibration:<br> BMRA_Cryo_run5<br> BMRA_Cryo_run6</p> <p>MD simulations of BMRA + R6G:<br> BMRA_R6G_run1<br> BMRA_R6G_run2<br> BMRA_R6G_run3</p> <p> </p>
Molecular dynamics simulation data of stapled peptides
<p>Molecular dynamics simulations for Axin and HIV peptides.</p>
Molecular dynamics trajectory files
<p>Molecular dynamics trajectory files</p>
Molecular Dynamics Simulations of HADDOCK-predicted Complex Structures of apoE2 and Factor H
<p>Input and output data for the molecular dynamics simulations of the FH5–7/ApoE2 complex. Initial structures generated with the HADDOCK v2.4 web server with 3 nm distance restraints for lysine pairs that were experimentally found to be cross-linked with DSS. </p> <p>Five clusters and the four representative structures provided by HADDOCK were then used for atomistic molecular dynamics simulations. These structures were solvated and simulated with both CHARMM36m and Amber FF14SB force fields for 250 ns each using GROMACS 2021. The recommended simulation parameters were used for both force fields, and they are available in the mdp files. </p> <p>For each of these 5 (clusters) x 4 (structures per cluster) x 2 (force fields) = 40 simulations, the outputs and inputs are provided; the trajectory (xtc), energy file (edr), final structure (gro), run parameter file (tpr), and continue point (cpt) are system-specific, whereas a single topology (top) and index file (ndx) is shared among all simulations with the same force field. The molecule definitions (itp) referred to in the topology are provided in the compressed files.</p>
Molecular Dynamics Simulation of CO2 Hydrate Growth in NaCl Aqueous Solution
<p>VIDEO for <a href="https://doi.org/SPE-214332-PA">https://doi.org/SPE-214332-PA</a>17</p>
Fig. 4 in Study of two isoforms of lipoxygenase by kinetic assays, docking and molecular dynamics of a specialised metabolite isolated from the aerial portion of Lithrea caustica (Anacardiaceae) and its synthetic analogs
Fig. 4. (Z)-3-(pentadec-10′-enyl)-catechol (1) and 3-pentadecylcatechol (2) Lineweaver-Burk graphs.
Fig. 1 in Study of two isoforms of lipoxygenase by kinetic assays, docking and molecular dynamics of a specialised metabolite isolated from the aerial portion of Lithrea caustica (Anacardiaceae) and its synthetic analogs
Fig. 1. Basic structure of urushiol.
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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.