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21,281 results for “Molecular”
Dataset For Molecular Dynamics Simulations of Thin Film Rupture
<p>Data files for production runs for the key results reported in "Life and Death of a Thin Liquid Film", (2024) by Muhammad Rizwanur Rahman, Li Shen, James P. Ewen, D. M. Heyes, Daniele Dini, and E. R. Smith. The directory named "spontaneous-rupture-equilibrated-state-for-production-runs" contains data files of different initial film thicknesses, and the directory named "synthetic-rupture-equilibrated-state-for-production-runs" contains data files for films with similar initial thickness, but with different patterns of synthetic damages caused to the film. These files should be used as the restart file for production phase under NVE ensemble. </p> <p>Codes to run these files, and process the data are described in github: https://github.com/MuhammadRRahman/Thin-Film-Rupture-NEMD.git.</p>
Rapid structure determination of microcrystalline molecular compounds using electron diffraction (nanoArgovia Project A3EDPI)
<p>The are the data linked to the publication "Rapid structure determination of microcrystalline molecular compounds using electron diffraction", <a href="https://doi.org/10.1002/anie.201811318">10.1002/anie.201811318</a>. Electron Diffraction data collected with an EIGER X 1M detector (DECTRIS Ltd.).</p> <p>Each tar file contains the raw files in HDF5 format, together with the XDS.INP file used for data integration. Images of the respective crystals have '_img_' in their file names. The log files for recording the stage alpha angle are included with the same name and suffix .txt. See publication for details.</p> <p>NB: The meta-data in the HDF5 files have no meaning, please refer to the respective XDS.INP file for respective information.</p> <p>The crystallographic data (CIF-files) have been uploaded to the ICSD (High--throughput Structural Chemistry with Electron Diffraction) and CSD (https://www.ccdc.cam.ac.uk/) respectively:</p> <p>Paracetamol from Grippostad CCDC 1856579<br> electron structure of MBBF4 CCDC 1856580</p> <p>ZSM-5 x227 CSD 1856581</p> <p>ZSM-5 x331 CSD 1856582</p> <p>ZSM-5 x79 CSD 1856583<br> ZSM-5 x811 CSD 1856584</p> <p> </p>
Multi-omic Insights into Molecular Mechanism and Therapeutic Targets in Spinocerebellar Ataxia type 7
<p>The molecular mechanism in spinocerebellar ataxia type 7 is currently poorly understood. To provide understandings, a multi-omic study was performed using SCA7266Q/5Q mice. At week 12, entire brain tissue samples were collected and RNA sequencing, methylation analysis, and proteomic analysis were performed. Results were integrated to identify genes with identical trends in expression. Data was also compared with SCA patient serum proteomic analysis, and based on common differentially expressed proteins, a Naïve Bayesian network model was constructed to predict nilotinib treatment response. Data from RNA sequencing and methylation analysis revealed 58 significantly hypomethylated-upregulated genes and 62 hypermethylated-downregulated genes, mostly enriched in GO terms of regulation of axonogenesis, channel activity, and monoamine signaling. In the proteomic analysis, 211 upregulated and 281 downregulated DEPs associated mostly with immune response and cellular mobility were identified. Two genes, Fam107b and Tph2, showed differential expression in both transcriptomic and proteomic analysis. Forty-two overlapping proteins were identified compared with SCA patient serum, and Bayesian network analysis revealed that nilotinib treatment response was associated with the protein expression of CLU, CA2, GLUL, PRDX6, C1QA, PLXNB1, and age. These findings will serve as an important reference for future studies on the pathogenesis and discovery of druggable targets. </p>
Molecular Interactions of Photosystem I and ZIF-8 in Bio-Nanohybrid Materials
<p>Supporting data for the article "Molecular Interactions of Photosystem I and ZIF-8 in Bio-Nanohybrid Materials", published in Physical Chemistry Chemical Physics (DOI: <span> <a href="https://doi.org/10.1039/D4CP03021D">10.1039/D4CP03021D)</a></span></p>
Growth of hexagonal boron nitride from molten nickel solutions: a reactive molecular dynamics study
<p>Authors: Amin Ahmadisharaf and Jeffrey Comer</p> <p><br>Publication: Amin Ahmadisharaf, Bin Liu, James H. Edgar, and Jeffrey Comer (2025) Growth of Hexagonal Boron Nitride from Molten Nickel Solutions: A Reactive Molecular Dynamics Study. ACS Applied Materials & Interfaces. <a href="https://doi.org/10.1021/acsami.4c16991">doi.org/10.1021/acsami.4c16991</a></p> <p>Funding: Department of Energy Office of Science, grant DE-SC0021264, <a>https://pamspublic.science.energy.gov/WebPAMSExternal/Interface/Common/ViewPublicAbstract.aspx?rv=5e6ffff5-0daa-47e8-a3d0-20f594b7bfb8&rtc=24&PRoleId=10</a></p> <p>**************************************</p> <p>This data set for the manuscript entitled "Growth of Hexagonal Boron Nitride from Molten Nickel Solutions: A Reactive Molecular Dynamics Study" includes all files needed to run and analyze the simulations described in the this manuscript in the molecular dynamics software LAMMPS, as well as the output of the simulations. The files are organized into directories corresponding to the figures of the main text. They include force field parameter files (in ReaxFF format), LAMMPS configuration files (*.in), ReaxFF control files (*.control), LAMMPS log files (*.log), and LAMMPS output including restart files (in binary LAMMPS format) and trajectories in dcd format (downsampled to 12.5 or 25 ps per frame) and also PDB and PSF files are useful for visualization with VMD. Analysis is performed by python and shell scripts (Bash-compatible) that call VMD Tcl scripts or python scripts. These scripts and their output are also included.</p> <p>The species analysis is performed by the VMD Tcl script "Figure3/analysis/count_hBN_species_NNB_BN.tcl" using the parameters given in "Figure3/analysis/doCount.sh".</p> <p>The directory contents are as follows.</p> <p>--------------------------------------------------------------<br>Figure-1: Parallel tempering simulations of the boron-nickel system and calculation of the boron concentration along the z-dimension of the nickel slab.</p> <p>The analysis of the boron concentration profile is performed by the VMD Tcl scripts calcRatioZRef.tcl and calcConcZRef.tcl using the parameters given in "Figure1/analysis/step3_conc_profile.sh". Also, the reorganization of the parallel tempering trajectories into frames at a single temperature is performed by the VMD Tcl script extractReplicaFrames.tcl based on "Figure1/analysis/step1_sort_frames.sh".</p> <p><br>--------------------------------------------------------------<br>Figure-2: Simulation of hBN sheet growth at 1750 K and calculation of largest cluster.</p> <p><br>--------------------------------------------------------------<br>Figure-3: Simulations of different boron-to-nickel ratios at varying nitrogen pressures at 1750 K and the calculation of the largest hBN cluster formed under different scenarios. The suffixes "liu", "long_liu", and "low_liu" correspond to pressures of 100.0, 50.0, and 25.0 atm respectively.</p> <p>The analysis of hBN clusters is performed by the VMD Tcl script "Figure3/analysis/" using the parameters given in "Figure3/analysis/doCount.sh". The related simulations files and outputs for panel A in this figure are located in Figure 5 directory.</p> <p><br>--------------------------------------------------------------<br>Figure-4: Recognition and counting the different boron-nitrogen motifs in the simulation was performed in Figure 2.</p> <p>The related simulations files and outputs for panel B and C in this figure are located in Figure 5 directory.</p> <p><br>--------------------------------------------------------------<br>Figure-5: Simulation of the temperature effect on hBN growth, and recognition and counting of the different boron-nitrogen motifs at 1750, 1800, 1900, 2000, 2200, and 2700 K.. </p> <p><br>--------------------------------------------------------------<br>Figure-6: Recognition of existing motifs for nitrogen atoms in the growth path of hBN and calculation of the probabilities of transitions between different motifs across all nitrogen atoms.</p> <p>The related simulations files and outputs for all panels in this figure are located in Figure 5 directory.</p> <p><br>--------------------------------------------------------------<br>Figure-7: Comparing the ReaxFF and ab initio simulations of small B-N motifs(B--N--B and B--N) in a nickel slab and calculation of bond lengths and angle values.</p> <p><br>--------------------------------------------------------------<br>Figure-8: Diffusion simulations of four different systems at 1800 K: nickel with a single B atom, nickel with a single N atom, nickel with a free B-N-B molecule, and nickel with a small hBN sheet and Mean Squared Displacement (MSD) values were calculated and compared to assess the surface mobility of the different particles.</p> <p> </p>
Dataset: Insight in molecular degradation patterns and co-metabolism during rose waste co-composting
<p>This dataset and these scripts supports the article 'Insight in molecular degradation patterns and co-metabolism during rose waste co-composting' as published in Biogeochemistry. https://doi.org/10.1007/s10533-023-01092-1</p> <p>Roses are an important crop for the floricultural sector of Kenya and roses are a perennial crop and under continuous production for six to ten years. The cultivation produces large quantities of green waste, up to 50 kg per hectare per day. In this experiment we aimed to gain insight in the decomposition patterns underlying rose waste composting and to identify co-metabolisms of ligneous materials. Samples were taken during a six-month experiment and analyzed by pyrolysis-GC/MS (see manuscript for analytical details).</p>
The Data Related to Interfacial Shift Keying Allows a High Information Rate in Molecular Communication
<p>This dataset is related to a method for molecular communication in fluids described on "Fluorescent nanoparticles for reliable communication among implantable medical devices," Carbon, vol. 190, pp. 262-275, Apr. 2022, by Federico Calì, Luca Fichera, Giuseppe Trusso Sfrazzetto, Giuseppe Nicotra, Gianfranco Sfuncia, Elena Bruno, Luca Lanzanò, Ignazio Barbagallo, Giovanni Li-Destri, Nunzio Tuccitto; doi: 10.1016/J.CARBON.2022.01.016. <br> The dataset is linked to the manuscript entitled "Interfacial Shift Keying Allows a High Information Rate in Molecular Communication: Methods and Data" by F. Calì, G. Li-Destri, and N. Tuccitto submitted to IEEE Transactions on Molecular, Biological, and Multi-Scale Communications (T-MBMC).<br> The data, including elapsed time (s), starting from the injection and fluorescence intensity (a.u.), is given in tab-separated values format as .txt files. When present, a column includes the intensity subtracted for the baseline and the subtracted and normalized intensity. In all cases, the baseline was obtained by performing a linear fit between 10 and 110 s and subtracting the line obtained from the entire dataset.<br> </p>
Molecular mechanism for the synchronized electrostatic coacervation and co-aggregation of alpha-synuclein and tau
<p><strong><em>The following metadata refers exclusively to electron paramagnetic resonance (EPR) measurements, which represent the contribution of the PARACAT students to this work</em></strong></p> <ul> <li><strong>Data type</strong>: EPR spectroscopic measurements and simulations</li> <li>Files are in <strong>.DTA, .DSC, .m, .mat, and .xlxs, </strong>formats</li> <li>Information on <strong>origin of the data</strong>: <ul> <li>EPR spectroscopic measurements in <strong>.DTA </strong>and<strong> .DSC</strong> formats</li> <li>EPR spectroscopic simulation and analyses in .<strong>m </strong>and<strong> .mat</strong> format</li> <li>“Ready-to-plot”, processed EPR spectra are in <strong>.xlxs</strong> format.</li> </ul> </li> <li>The data are <strong>generated</strong> by: <ul> <li>CW-EPR measurements were performed with a Bruker ELEXSYS E580 X-band spectrometer equipped with a Bruker ER4118 SPT-N1 resonator operating at a microwave (MW) frequency of ∼9.7 GHz. The temperature was set to 25 °C and controlled by a liquid nitrogen cryostat.</li> </ul> </li> </ul> <p> </p> <ul> <li><strong>If the dataset includes multiple files that relate to each other:</strong> <ul> <li>Files in <strong>PARACAT_WP3_20221219_EPR </strong>folder includes EPR spectroscopic measurements and computer simulations/analyses, original data are in <strong> .DTA/.DSC</strong> formats; files in .<strong>m</strong> format were used to process the data.</li> </ul> </li> </ul> <p>NB. See the “READ ME” text file for more detailed information on files organization.</p> <p> </p> <ul> <li><strong>Information on</strong>: <ul> <li>Abbreviations: <ul> <li><strong>avg</strong> = averaged</li> <li><strong>aS_24</strong> = alpha-synuclein protein with TEMPOL spin label at position 24 of the polypeptidic chain</li> <li><strong>aS_122</strong> = alpha-synuclein protein with TEMPOL spin label at position 122 of the polypeptidic chain</li> <li><strong>pLK</strong> = poly-lysine</li> <li><strong>Tau441</strong> = Tau protein with complete amino-acid sequence</li> <li><strong>Tau_DNt</strong> = truncated Tau protein lacking N-terminal (see paper methods for further details)</li> </ul> </li> <li>Units of measurement: <ul> <li>Temperature: <strong>°</strong><strong>C</strong> (Celsius)</li> <li>Microwave Frequency: <strong>GHz</strong> (Giga-Hertz), <strong>MHz</strong> (Mega-Hertz), <strong>kHz</strong> (kilo-Hertz)</li> <li>Microwave Power: <strong>mW</strong> (milli-Watt)</li> <li>Magnetic Field: <strong>mT</strong> (milli-Tesla)</li> <li>Time: <strong>s</strong> (seconds)</li> <li>Concentration: <strong>μM</strong> (micro-Molar), <strong>% w/v</strong> (percentage weight-volume)</li> </ul> </li> </ul> </li> </ul>
CHIKVnext: Molecular epidemiology of Chikungunya virus
<p>CHIKVnext is an interactive resource to study the evolution and global spread of Chikungunya virus (CHIKV), built on the Nextstrain platform.</p>
Molecular and functional properties of human Plasmodium falciparum CSP C-terminus antibodies
<p>AIRR Community-compliant information comprising all antibodies described in EMBO Mol Med 15:e17454 [DOI:10.15252/emmm.202317454].</p>
Molecular Maquettes of the Pyrite Surface Sites
<p>The dataset provides an introductory level representation of the <em>n</em>(FeS<sub>2</sub>)<sub>(p)</sub> nanoparticles with <em>n</em>=4, <em>n</em>=8, <em>n</em>=18, and <em>n</em>=32 Fe ions. In addition to the paramagnetic and coupled peripheral Fe ions, the latter two compositions involve one and six, low spin, bulk Fe<sup>2+</sup> sites as in the pyrite crystal structure.</p> <p>Calculations were carried out at the MN15/def2SVP level along with all models being embedded into a polarizable continuum model (SMD). The zip files contain representative files that support the XYZ Cartesian Coordinate files. They include spin density contour plots, formatted checkpoint files, the corresponding cube and the output files. Initial model structures were created using the high resolution, low temperature crystal structure</p> <p>An extension is being curated in order to disseminate the structure and electronic properties/features of these nano-scale models of reactive pyrite surfaces.</p> <p>Please stay tuned for further updates ...</p>
Supplementary data: Agro-morphological and molecular characterization reveal deep insights in promising genetic diversity and marker-trait associations in Fagopyrum esculentum and F. tataricum
<p>Our study focuses on the global/European buckwheat germplasm collected as part of the ECOBREDD project. The potential of this highly diverse collection for organic buckwheat breeding was evaluated at two complementary levels: phenotypic and genetic. Here, we characterized the phenotypic and genetic diversity of a global collection of the two cultivated buckwheat species <em>Fagopyrum esculentum</em> and <em>F. tataricum</em> (190 and 51 accessions, respectively) using 37 agro-morphological traits and 24 SSR markers (Simple Sequence Repeats) (see publication and info sheet of the data).</p>
Dataset for Machine Learning Framework for Modeling Exciton-Polaritons in Molecular Materials
<p>The data consists of several NumPy arrays saved in the binary format (npy files) with a total size of 108 MB. The details of these files are listed below.</p> <table> <tbody> <tr> <td> <p><strong>Filename and path</strong></p> </td> <td> <p><strong>Description</strong></p> </td> </tr> <tr> <td> <p>training/azo_R.npy</p> </td> <td> <p>Coordinates for training</p> </td> </tr> <tr> <td> <p>training/azo_Z.npy</p> </td> <td> <p>Atomic indices for training</p> </td> </tr> <tr> <td> <p>training/azo_E.npy</p> </td> <td> <p>Molecular energies for training</p> </td> </tr> <tr> <td> <p>training/azo_D.npy</p> </td> <td> <p>Transition dipoles for training</p> </td> </tr> <tr> <td> <p>training/azo_ScaledNACR.npy</p> </td> <td> <p>Non-adiabatic coupling vectors scaled by energy difference for training</p> </td> </tr> <tr> <td> <p>scan/azo_R.npy</p> </td> <td> <p>Coordinates for PES scan</p> </td> </tr> <tr> <td> <p>scan/azo_Z.npy</p> </td> <td> <p>Atomic indices for PES scan</p> </td> </tr> <tr> <td> <p>scan/azo_E.npy</p> </td> <td> <p>Molecular energies for PES scan</p> </td> </tr> <tr> <td> <p>scan/azo_D.npy</p> </td> <td> <p>Transition dipoles for PES scan</p> </td> </tr> <tr> <td> <p>scan/azo_ScaledNACR.npy</p> </td> <td> <p>Non-adiabatic coupling vectors scaled by energy difference for PES scan</p> </td> </tr> <tr> <td> <p>spectrum/azo_R.npy</p> </td> <td> <p>Coordinates for spectrum calculations</p> </td> </tr> <tr> <td> <p>spectrum/azo_Z.npy</p> </td> <td> <p>Atomic indices for spectrum calculations</p> </td> </tr> <tr> <td> <p>spectrum/azo_E.npy</p> </td> <td> <p>Molecular energies for spectrum calculations</p> </td> </tr> <tr> <td> <p>spectrum/azo_D.npy</p> </td> <td> <p>Transition dipoles for spectrum calculation</p> </td> </tr> </tbody> </table>
Molecular and Taxonomic Reevaluation of the Digitaria filiformis Complex (Poaceae) including a Globally Extinct, Single Site Endemic from New Hampshire, USA, and a New Species from Mexico
<p>We examine the <em>Digitaria filiformis </em>complex, to determine the proper taxonomic rank and rarity of each taxon. The taxonomy of the <em>D. filiformis </em>complex is highly debated and includes two widespread species, <em>D. filiformis </em>and <em>D. villosa</em>; a possibly extinct species endemic to a single-site in New Hampshire, <em>D. laeviglumis</em>; and a rare species of southern Florida and the West Indies, <em>D.</em><em> dolichophylla. </em>We conducted morphologic comparisons and molecular analysis of the four members of the <em>D. filiformis</em> complex, together with specimens from Mexico and Venezuela purportedly identified as <em>D. laeviglumis</em> (morphology only). Based on results of phylogenetic analyses of plastid and nuclear ITS sequences and morphologic comparisons, we recognize five species in the <em>D. filiformis </em>complex, including a newly described Mexican endemic <em>D. glabrifloris. </em>After field investigation we have moved the global rank of <em>D. laeviglumis </em>from globally historical (GH) to extinct (GX), as there is virtually no likelihood of rediscovery. <em>Digitaria</em><em> dolichophylla </em>is much rarer than previously recognized, moving from secure (T5) to imperiled with extinction (G2).</p>
MCR LTER: Coral Reef: Distinguishing the molecular diversity, nutrient content, and energetic potential of exometabolomes produced by macroalgae and reef-building corals; data for Kelly et al., 2022 PNAS
Metabolites exuded by primary producers comprise a significant fraction of marine dissolved organic matter, a poorly characterized, heterogenous mixture that dictates microbial metabolism and biogeochemical cycling. We present a foundational untargeted molecular analysis of exudates released by coral reef primary producers using liquid chromatography–tandem mass spectrometry to examine compounds produced by two coral species and three types of algae (macroalgae, turfing microalgae, and crustose coralline algae [CCA]) from Mo’orea, French Polynesia. Of 10,568 distinct ion features recovered from reef and mesocosm waters, 1,667 were exuded by producers; the majority (86%) were organism specific, reflecting a clear divide between coral and algal exometabolomes. These data allowed us to examine two tenets of coral reef ecology at the molecular level. First, stoichiometric analyses show a significantly reduced nominal carbon oxidation state of algal exometabolites than coral exometabolites, illustrating one ecological mechanism by which algal phase shifts engender fundamental changes in the biogeochemistry of reef biomes. Second, coral and algal exometabolomes were differentially enriched in organic macronutrients, revealing a mechanism for reef nutrient-recycling. Coral exometabolomes were enriched in diverse sources of nitrogen and phosphorus, including tyrosine derivatives, oleoyl-taurines, and acyl carnitines. Exometabolites of CCA and turf algae were significantly enriched in nitrogen with distinct signals from polyketide macrolactams and alkaloids, respectively. Macroalgal exometabolomes were dominated by nonnitrogenous compounds, including diverse prenol lipids and steroids. This study provides molecular-level insights into biogeochemical cycling on coral reefs and illustrates how changing benthic cover on reefs influences reef water chemistry with implications for microbial metabolism. This material is based upon work supported by the U.S. National Science Founda
Logical model for Molecular Pathways Enabling Tumour Cell Invasion and Migration
<p>Understanding the etiology of metastasis is very important in clinical perspective, since it is estimated that metastasis accounts for 90% of cancer patient mortality. Metastasis results from a sequence of multiple steps including invasion and migration. The early stages of metastasis are tightly controlled in normal cells and can be drastically affected by malignant mutations; therefore, they might constitute the principal determinants of the overall metastatic rate even if the later stages take long to occur. To elucidate the role of individual mutations or their combinations affecting the metastatic development, a logical model has been constructed that recapitulates published experimental results of known gene perturbations on local invasion and migration processes, and predict the effect of not yet experimentally assessed mutations. The model has been validated using experimental data on transcriptome dynamics following TGF-β-dependent induction of Epithelial to Mesenchymal Transition in lung cancer cell lines. A method to associate gene expression profiles with different stable state solutions of the logical model has been developed for that purpose. In addition, we have systematically predicted alleviating (masking) and synergistic pairwise genetic interactions between the genes composing the model with respect to the probability of acquiring the metastatic phenotype. We focused on several unexpected synergistic genetic interactions leading to theoretically very high metastasis probability. Among them, the synergistic combination of Notch overexpression and p53 deletion shows one of the strongest effects, which is in agreement with a recent published experiment in a mouse model of gut cancer. The mathematical model can recapitulate experimental mutations in both cell line and mouse models. Furthermore, the model predicts new gene perturbations that affect the early steps of metastasis underlying potential intervention points for innovative therapeutic strategies in oncology.</p> <p> </p> <p>Included files:</p> <ul> <li>Master Model: the model includes detailed regulation of the major players involved in the crosstalks between Notch and p53 pathways</li> <li>Modular Model: the model is a reduction of the master model. To reduce the master model, we lumped together some entities that belonged to a module.</li> </ul>
All-atom 500-nano seconds Molecular Dynamics Simulations of SARS-CoV-2 Spike Receptor-binding Domain bound with ACE2
<p>Data includes all of the trajectories (1000) of classical all-atom molecular dynamics (MD) simulations of of SARS-CoV2 Spike Protein/ACE2 complex (PDB ID: 6M0J). In order to decrease the size of the file only protein rajectories were provided. Simulation has been performed with Desmond. Protein was placed in the cubic boxes with explicit TIP3P water models that have 10.0 Å thickness from surfaces of protein. The system is neutralized by adding counter ions, and salt solution of 0.15M NaCl was also used to adjust the concentration of the systems. The long-range electrostatic interactions were calculated by the particle mesh Ewald method. A cutoff radius of 9.0 Å was used for both van der Waals and Coulombic interactions. The temperature was set as 310K initially, and Nose–Hoover thermostat was used for adjustment. Martyna–Tobias–Klein protocol was employed to control the pressure, which was set at 1.01325 bar. The time-step was assigned as 2.0 fs. The default values were used for minimization and equilibration steps, and finally 500 nano-seconds (ns) production run was performed for the simulation.</p>
Data from: "Rapid molecular evolution of Spiroplasma symbionts of Drosophila"
<p>This repository contains data and information to reproduce the findings reported in the paper.</p> <p>File descriptions:</p> <ul> <li>OTU_sequences.fasta – all <em>Spiroplasma</em> sequences that contained an <a href="https://pfam.xfam.org/family/OTU">OTU domain</a> as predicted by <a href="https://www.ebi.ac.uk/Tools/pfa/pfamscan/">PfamScan</a></li> <li>OTU_alignments.fasta – alignment of OTU domains performed using <a href="https://mafft.cbrc.jp/alignment/software/">Mafft</a></li> <li>RIP_sequences.fasta – all <em>Spiroplasma</em> sequences that contained an <a href="https://pfam.xfam.org/family/RIP">RIP domain</a> as predicted by <a href="https://www.ebi.ac.uk/Tools/pfa/pfamscan/">PfamScan</a></li> <li>RIP_alignments.fasta – alignment of RIP domains performed using the <a href="http://hmmer.org/">HMMER package</a></li> <li>Spiroplasma_supermatrix.fasta – Fasta alignment of concatenated single copy <em>Spiroplasma</em> loci conserved across the investigated strains. Loci that showed signs of recombination were not included</li> <li>Spiroplasma_partitions.txt – Lists the loci that make up the <em>Spiroplasma</em> supermatrix</li> <li>Spiroplasma_partitioning.scheme.txt – Partitioning scheme employed in our Maximum Likelihood analysis of the supermatrix. This was the best fitting partitioning scheme as determined with <a href="http://www.iqtree.org/">IQ-TREE</a></li> <li>Protocol_1.pdf – Chloroform–Ethanol protocol used for extracting <em>Spiroplasma</em> DNA for <em>s</em>Hy-Tx</li> </ul>
Representative Structures from Molecular Dynamics Simulations of the Inward Facing and Outward Facing States of LaINDY
<p>This upload is a supplementary data set for the following publication: <a href="https://doi.org/10.7554/eLife.61350">D. B. Sauer, N. Trebesch, J. J. Marden, N. Cocco, J. Song, A. Koide, S. Koide, E. Tajkhorshid, and D.-N. Wang. "Structural basis for the reaction cycle of DASS dicarboxylate transporters." <em>eLife</em>. <strong>9</strong>, e61350. DOI: 10.7554/eLife.61350</a>. Please see the main publication for the methods, analysis, and discussion associated with this data set.</p>
Broadband Dielectric Spectroscopy Study of Biobased Poly(alkylene 2,5-furanoate)s' Molecular Dynamics
<p><strong>Related publication:</strong><br> Soccio, M.; Martínez-Tong, D.E.; Guidotti, G.; Robles-Hernández, B.; Munari, A.; Lotti, N.; Alegria, A. Broadband Dielectric Spectroscopy Study of Biobased Poly(alkylene 2,5-furanoate)s’ Molecular Dynamics. <em>Polymers</em> 2020, <em>12</em>, 1355.<br> <a href="https://doi.org/10.3390/polym12061355">10.3390/polym12061355</a></p> <p><strong>EUSMI proposal codes:</strong><br> E171100040, E171100043</p>
ScienceDex guides
Understand access before you commit
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.