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3,878 results for “Molecular data”
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>
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>
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>
Benchmark Data for Attracting Cavities 2.0 Small-Molecular Docking Program
<p>This repository provides data from the following article:<br> <br> U.F. Roehrig, M. Goullieux, M. Bugnon, V. Zoete,<br> Attracting Cavities 2.0: Improving the Flexibility and Robustness for Small-Molecule Docking.<br> J. Chem. Inf. Modeling 2023<br> https://doi.org/10.1021/acs.jcim.3c00054<br> <br> </p>
TUK-FFDat - Data scheme and data format for transferable force fields for molecular simulation
<p>Online repository to suplement the following publication:</p> <p>G. Kanagalingam, S. Schmitt, F. Fleckenstein, S. Stephan: Data scheme and data format for transferable force fields for molecular simulation, Scientific Data, accepted (2023).</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>
Fig. 3 in A new western Atlantic snapping shrimp of the Alpheus macrocheles group (Caridea, Alpheidae) revealed by morphological, molecular and color data
Fig. 3. Alpheus ramosportoae sp. nov., paratype, ♂, from seamounts of the North Chain, Ceará, northeastern Brazil (MOUFPE 13703). A. Second pereiopod, lateral view. B. Third pereiopod, lateral view. C. Fourth pereiopod, lateral view. D. Fifth pereiopod, lateral view. E–G. Third to fifth pereiopods, detail of propodus, lateral view. H–I. Third and fourth pereiopods, detail of dactylus. Scale bars: A–G = 0.5 mm; H–I = 0.25 mm.
Fig. 1 in A new western Atlantic snapping shrimp of the Alpheus macrocheles group (Caridea, Alpheidae) revealed by morphological, molecular and color data
Fig. 1. Alpheus ramosportoae sp. nov. A–D. Holotype, ♂, from off Recife, state of Pernambuco, northeastern Brazil (MOUFPE 19470). A. Carapace and cephalic appendages, dorsal view (setae omitted). B. Same, lateral view. C. Tooth on ventromesial carina of antennular peduncle. D. Left mandible, mesial view. E–L. Paratype, ♂, from seamounts of the North Chain, Ceará, northeastern Brazil (MOUFPE 13703). E. First maxilla, lateral view. F. Second maxilla, lateral view. G. First maxilliped, lateral view. H. Second maxilliped, lateral view. I. Third maxilliped, lateral view. J. Telson and uropods, dorsal view (setae omitted). K. Uropod, detail of the distolateral angle of the exopod. L. Uropod, detail of the posteerior margin of endopod. Scale bars: A–B, J = 1 mm; C–I, K–L = 0.5 mm.
Molecular dynamics simulation data of designed cyclic peptide (ligand-only)
<p>Trajectories of <strong>ligand-only </strong>simulation and simulation set-up files of designed cyclic peptide as MDM2 binders. <br> The original paper of these designed cyclic peptide: Danelius, E., Pettersson, M., Bred, M., Min, J., Waddell, M. B., Guy, R. K., et al. (2016). Flexibility is important for inhibition of the MDM2/p53 protein–protein interaction by cyclic β-hairpins. <em>Org. Biomol. Chem.</em>, <em>14</em>(44), 10386–10393. http://doi.org/10.1039/C6OB01510G</p>
Molecular dynamics simulation data of regulatory ACT domain dimer of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer.</p> <p><strong>binding.zip</strong>: simulation starting from 21 dimer conformations with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation starting from dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation starting from 21 dimer conformations simulation</p> <p>Simulation setup files are also included in each folder.</p> <p>Details can be found in this paper:</p> <p><strong>Yunhui Ge</strong>, Elias Borne, Shannon Stewart, Michael R. Hansen, Emilia C. Arturo, Eileen K. Jaffe and Vincent A. Voelz. <a href="http://www.jbc.org/content/293/51/19532"><em>Simulation of the regulatory ACT domain of human PAH unveil the mechanism of phenylalanine binding.</em></a> J. Biol. Chem., 2018, 293(51), pp 19532-19543</p>
Molecular dynamics simulation data of regulatory ACT domain monomer of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain monomer.</p> <p><strong>binding.zip</strong>: simulation starting from 21 monomer conformations with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation starting from monomer with bound Phe ligand</p> <p><strong>monomer_only.zip</strong>: simulation starting from 21 monomer conformations simulation</p> <p>Simulation setup files are also included in each folder. Adaptive sampling data are also included in <strong>monomer </strong>and <strong>binding</strong> simulations.</p> <p>Details can be found in this paper:</p> <p><strong>Yunhui Ge</strong>, Elias Borne, Shannon Stewart, Michael R. Hansen, Emilia C. Arturo, Eileen K. Jaffe and Vincent A. Voelz. <a href="http://www.jbc.org/content/293/51/19532"><em>Simulation of the regulatory ACT domain of human PAH unveil the mechanism of phenylalanine binding.</em></a> J. Biol. Chem., 2018, 293(51), pp 19532-19543</p>
Molecular dynamics simulation data of designed β-hairpins
<p>Raw simulations data (protein only) and simulation set-up files of designed β-hairpins. More details can be found in this paper: </p> <p>Yunhui Ge, Brandon Kier, Niels H. Andersen and Vincent A. Voelz. <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.7b00132"><em>Computational and experimental evaluation of designed beta-cap hairpins using molecular simulations and kinetic network models.</em></a> J. Chem. Inf. Model., 2017, 57 (7), pp 1609–1620</p>
Replica exchange molecular dynamics simulation data of designed β-hairpins (implicit solvent, AMBER ff96)
<p>Raw REMD simulation data (protein only) of designed β-hairpins. AMBER ff96 and implicit solvent model is used. More details can be found in this paper: </p> <p>Yunhui Ge, Brandon Kier, Niels H. Andersen and Vincent A. Voelz. <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.7b00132"><em>Computational and experimental evaluation of designed beta-cap hairpins using molecular simulations and kinetic network models.</em></a> J. Chem. Inf. Model., 2017, 57 (7), pp 1609–1620</p>
Replica exchange molecular dynamics simulation data of designed β-hairpins (implicit solvent, AMBER ff99SB-ildn)
<p>Raw REMD simulation data (protein only) of designed β-hairpins. AMBER ff99SB-ildn and implicit solvent model is used. More details can be found in this paper: </p> <p>Yunhui Ge, Brandon Kier, Niels H. Andersen and Vincent A. Voelz. <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.7b00132"><em>Computational and experimental evaluation of designed beta-cap hairpins using molecular simulations and kinetic network models.</em></a> J. Chem. Inf. Model., 2017, 57 (7), pp 1609–1620</p>
Fig. 1 in A new species of Casmaria H. Adams & A. Adams, 1853 (Gastropoda, Cassidae) from the Philippines identified by molecular data
Fig. 1. Bayesian phylogenetic trees of studied members of the genus Casmaria obtained with standard genetic markers. Posterior probabilities when greater than 0.80 are indicated for each node. A. Phylogenetic tree based on the CO1 gene; for specimens underlined, vouchers are illustrated on the right. B. Phylogenetic tree based on the 16S rRNA gene. C. Phylogenetic tree based on the 12S rRNA gene.
Enhanced Molecular Spin-Photon Coupling at Superconducting Nanoconstrictions. Open data sets
<p>Includes data relevant for publication with DOI <a href="https://doi.org/10.1021/acsnano.0c03167">10.1021/acsnano.0c03167</a> plus a table with information on how the data were obtained and processed.</p>
Fig. 3 in New acoustic and molecular data shed light on the poorly known Amazonian frog Adenomera simonstuarti (Leptodactylidae): implications for distribution and conservation
Fig. 3. Preserved male of nominal Adenomera simonstuarti (Angulo & Icochea, 2010) (= genetic lineage 3): call voucher INPA-H 40967 (SVL = 23.4 mm) from the upper Juruá River, in Tarauacá, Brazilian state of Acre. This specimen corresponds to a call voucher (see Fig. 5). A−B. Body in dorsal and ventral views, not to scale. C−D. Detail of the ventral surface of right foot and hand, respectively. Note the nearly solid, dark-colored stripe along the underside of the forearm. Photographs by J. Magnusson. Scale bar = 5 mm.
Figure 2 in The contribution of molecular data to our understanding of cephalopod evolution and systematics: a review
Figure 2. Polyploidy scenario suggested by and reproduced from Bonnaud et al. (2004). Updated diploid chromosome numbers (see Table 2) for the various branches are now Nautiloidea 52; Octopoda 56–60; Sepiolida 74; Sepiida 48–112; Myopsida 86–92 (?22-?172).
Figure 6 in The contribution of molecular data to our understanding of cephalopod evolution and systematics: a review
Figure 6. Relationships among Sepiida. (A) Consensus tree based on 12S rRNA, 16S rRNA, cytochrome oxidase subunit II (Bonnaud et al. 2006); (B) maximum likelihood tree of cytochrome oxidase subunit I, cytochrome b and ND5 combined (Yoshida et al. 2010); (C) whole evidence approach using four to ten genes (Lindgren et al. 2012). Trees redrawn from original sources.
Figure 7 in The contribution of molecular data to our understanding of cephalopod evolution and systematics: a review
Figure 7. Relationships within Onychoteuthidae. (A) Neighbour-joining tree based on 16S ribosomal RNA (Bonnaud et al. 1998); (B) maximum likelihood tree of five genes (see text) combined (Lindgren 2010); (C) maximum likelihood tree based on whole evidence approach using four to ten genes (Lindgren et al. 2012). All trees redrawn from original sources. Nomenclature uses systematic revision of Bolstad (2010).
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.