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3 results for “hydrogen-deuterium exchange”
Underlying data for "Interpretation of Hydrogen-Deuterium Exchange Data by Maximum-Entropy Reweighting of Simulated Structural Ensembles"
<p>This dataset contains code, data, and figures used in the article "Interpretation of Hydrogen-Deuterium Exchange Data<br> by Maximum-Entropy Reweighting of Simulated Structural Ensembles".</p> <p>Contents:</p> <p>code/* - Underlying code used to analyze molecular dynamics trajectories and calculate predicted HDX-MS data, used to reweight structural ensembles to best fit target HDX-MS data, and used to structurally cluster simulation frames after reweighting</p> <p>data/* - Simulation trajectories of the TeaA protein, along with two sub-trajectories corresponding to only 'closed' or 'open' TeaA frames, and predicted HDX-MS deuterated fractions used as target data in simulation reweighting. Also simulation trajectories of the LeuT protein, in either 'outward-facing' or 'inward-facing' conformational states embedded in a DMPC bilayer, and experimental HDX-MS deuterated fractions used as target data in simulation reweighting</p> <p>figures/* - Underlying data and scripts used to create all figures and movies used in the article.</p> <p>Where appropriate, README files include instructions for regenerating data used in the article, and details of the Python packages used to run Python scripts are available in conda_environment.yml</p>
DNA-HDXMS_XchangeDB: A dataset of Hydrogen-Deuterium eXchange native Mass Spectrometry experiments on DNA oligonucleotides
<p>The DNA-HDXMS_XchangeDB dataset contains HDX/native MS exchange kinetics and metadata of a reference set of DNA oligonucleotides.</p> <p> </p>
Supplementary Movies: "Probing the dynamics of Streptococcus pyogenes Cas9 endonuclease bound to sgRNA complex using hydrogen-deuterium exchange mass spectrometry"
<p>Movies related to the article "Probing the dynamics of Streptococcus pyogenes Cas9 endonuclease bound to sgRNA complex using hydrogen-deuterium exchange mass spectrometry" in the International Journal of Molecular Science. "MD_Movie_Cas9_sgRNA_DNA" is the video of SpCas9-sgRNA-DNA complex behavior during 50 ns molecular dynamics simulation. In this movie, SpCas9 protein domains are shown in the following colors: REC lobe (green), CTD (blue), RuvC (pink), L-I-II (yellow), Arg (violet), and HNH (orange). RNA presented in cyan, and DNA -in dark blue.</p> <p>Movies "SpCas9_HeatMap" and "SpCas9-sgRNA_HeatMap" show the hydrogen exchange levels superimposed onto the protein structure obtained from MD trajectories. Relative uptake level presented at the time points of 10 s, 30 s, 1 min, 2 min, 5 min, 10 min, 30 min, 60 min, 120 min, 240 min, 360 min, and 480 min. The exchange scale is shown in a rainbow color scheme, where blue corresponds to the minimum uptake, while red corresponds to the highest observed uptake.</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.