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Dataset results
7 results for “XTC”
OpenMM simulations of POPE using the CHARMM Drude2023 force field in xtc format
<p>The dataset contains a PSF, a formatted coordinate file (CRD), and XTC files with the final 200 ns from<br> each of 3 replicate simulations from the paper</p> <p><br> <strong>Drude Polarizable Lipid Force Field with Explicit Treatment of LongRange Dispersion:<br> Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids</strong><br> Yalun Yu, Richard M. Venable, Jonathan Thirman, Payal Chatterjee, Anmol Kumar, Richard W. Pastor,*<br> Benoît Roux,* Alexander D. MacKerell, Jr.,* and Jeffery B. Klauda*<br> https://doi.org/10.1021/acs.jctc.3c00203</p> <p>XTC file names indicate the lipid and the replica number; each file has frames spaced at 10 ps over a 200 ns interval.</p> <p>The DCD sub-files in <span>10.5281/zenodo.7872447</span> have been concatenated into a single 200 ns long trajectory in xtc format by Batuhan Kav using MDAnalysis.</p>
OpenMM simulations of POPC using the CHARMM Drude2023 force field in xtc format
<p>PSF, single CRD file, and XTC format trajectories for the final 200 ns of triplicate POPC simulations, from the publication</p> <p><strong>Drude Polarizable Lipid Force Field with Explicit Treatment of LongRange Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids</strong><br> Yalun Yu, Richard M. Venable, Jonathan Thirman, Payal Chatterjee, Anmol Kumar, Richard W. Pastor,*<br> Benoît Roux,* Alexander D. MacKerell, Jr.,* and Jeffery B. Klauda*</p> <p> https://doi.org/10.1021/acs.jctc.3c00203</p> <p>XTC file names indicate the lipid and the replica number; each file has frames spaced at 10 ps over a 200 ns interval.</p> <p>The DCD sub-files in<span> 10.5281/zenodo.7871949 have been concatenated into a single 200 ns long trajectory in xtc format by Batuhan Kav using MDAnalysis.</span></p>
OpenMM simulations of DMPC using the CHARMM Drude2023 force field in xtc format
<p>The dataset contains a PSF, a formatted coordinate file (CRD), and XTC files with the final 200 ns from<br> each of 3 replicate simulations from the paper</p> <p><br> <strong>Drude Polarizable Lipid Force Field with Explicit Treatment of LongRange Dispersion:<br> Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids</strong><br> Yalun Yu, Richard M. Venable, Jonathan Thirman, Payal Chatterjee, Anmol Kumar, Richard W. Pastor,*<br> Benoît Roux,* Alexander D. MacKerell, Jr.,* and Jeffery B. Klauda*<br> https://doi.org/10.1021/acs.jctc.3c00203</p> <p>XTC file names indicate the lipid and the replica number; each file has frames spaced at 10 ps over a 200 ns interval.</p> <p>The DCD sub-files in <span>10.5281/zenodo.7872767</span> have been concatenated into a single 200 ns long trajectory in xtc format by Batuhan Kav using MDAnalysis.</p>
OpenMM simulations of DLPC using the CHARMM Drude2023 force field in xtc format
<p>The dataset contains a PSF, a formatted coordinate file (CRD), and XTC files with the final 200 ns from<br> each of 3 replicate simulations from the paper</p> <p><br> <strong>Drude Polarizable Lipid Force Field with Explicit Treatment of LongRange Dispersion:<br> Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids</strong><br> Yalun Yu, Richard M. Venable, Jonathan Thirman, Payal Chatterjee, Anmol Kumar, Richard W. Pastor,*<br> Benoît Roux,* Alexander D. MacKerell, Jr.,* and Jeffery B. Klauda*<br> https://doi.org/10.1021/acs.jctc.3c00203</p> <p>XTC file names indicate the lipid and the replica number; each file has frames spaced at 10 ps over a 200 ns interval.</p> <p>The DCD sub-files in <span>10.5281/zenodo.7872783</span> have been concatenated into a single 200 ns long trajectory in xtc format by Batuhan Kav using MDAnalysis.</p>
The NeXT Study; The Netherlands XTC Toxicity Study
ClinicalTrials.gov study NCT00235768. IPD Sharing: Not stated. Countries: 1. Publications: 7.
Supervised molecular dynamics for exploring the druggability of the SARS-CoV-2 spike protein (Topology and .xtc files)
<p>ABSTRACT. The recent outbreak of the respiratory syndrome-related coronavirus (SARS-CoV-2) is stimulating an unprecedented scientific campaign to alleviate the burden of the coronavirus disease (COVID-19). One line of research has focused on targeting SARS-CoV-2 proteins fundamental for its replication by repurposing drugs approved for other diseases. The first interaction between the virus and the host cell is mediated by the spike protein on the virus surface and the human angiotensin-converting enzyme (ACE2). Small molecules able to bind the receptor-binding domain (RBD) of the spike protein and disrupt the binding to ACE2 would offer an important tool for slowing, or even preventing, the infection. Here, we screened 2421 approved small molecules<em> in </em>silico and validated the docking outcomes through extensive molecular dynamics simulations. Out of six drugs characterized as putative RBD binders, the cephalosporin antibiotic cefsulodin was further assessed for its effect on the binding between the RBD and ACE2, suggesting the importance of considering the dynamic formation of the heterodimer when judging any potential candidate.</p>
OpenFF HMR Whole XTC
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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.