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289 results for “Molecular structure”
The three-dimensional structure of Galactic molecular cloud complexes out to 2.5 kpc
<p>Data files for Dharmawardena et al., accepted MNRAS, 2022, <em>The three-dimensional structure of Galactic molecular cloud complexes out to 2.5 kpc.</em></p> <p>In this works we map the Interstellar Dust Extinction and Density in 3D using <em>Dustribution</em> code: Dharmawardena et al., 2022, Astronomy & Astrophysics, Volume 658, id.A166, 30 pp. <a href="https://www.aanda.org/articles/aa/full_html/2022/02/aa41298-21/aa41298-21.html">https://www.aanda.org/articles/aa/full_html/2022/02/aa41298-21/aa41298-21.html</a></p> <p>The <em>Dustribution</em> code can be accessed from <a href="https://github.com/Thavisha/Dustribution">https://github.com/Thavisha/Dustribution</a></p> <p>The latest results from Dustribution can be interactively viewed and downloaded from <a href="https://www2.mpia-hd.mpg.de/homes/tmueller/projects/ThavishaDustDensity/index.html">https://www2.mpia-hd.mpg.de/homes/tmueller/projects/ThavishaDustDensity/index.html</a></p> <p>Data available here:</p> <p>- Trained gpy functions for all sixteen mapped regions which can be used to predict on any selected spherical or cartesian grid. </p> <p>-predicted cubes of 3D dust extinction and corresponding lbd boundary grids</p> <p>- predicted cubes of dust densities on cartesian grids and corresponding xyz boundary grids. </p> <p>- <em>astrodendro</em> derived dendrograms for all sixteen molecular cloud regions.</p> <p>- Tables of <em>astrodendro</em> produced parameters and calculated error bars for each region's substructure as described in appendix C of paper. </p> <p>- Tables 1,2,3 in main body of paper in .csv format. </p> <p>- 3D rendering videos of the sixteen mapped regions.</p>
Molecular dynamics simulations with grand-canonical reweighting suggest cooperativity effects in RNA structure probing experiments
<p>Molecular dynamics simulations of an RNA GAAA tetraloop interacting with SHAPE reagent 1-Methyl-7-nitroisatoic anhydride (1m7) in different numer of copies (1 to 19). See also https://arxiv.org/abs/2209.12640 and https://github.com/bussilab/paper-shapemd.</p>
Structural Dynamics of an Excited Donor-Acceptor Complex from Ultrafast Polarized Infrared Spectroscopy, Molecular Dynamics Simulations, and Quantum Chemical Calculations
<p>The files contains all the data that are shown in the figures of the article:</p> <p>Rumble, C.; Vauthey, E. Structural Dynamics of an Excited Donor-Acceptor Complex from Ultrafast Polarized Infrared Spectroscopy, Molecular Dynamics Simulations, and Quantum Chemical Calculations. Phys. Chem. Chem. Phys. 21 (2019). 10.1039/C9CP00795D</p>
Data from "Allostery and evolution: a molecular journey throught the structural and dynamical landscape of an enzyme super family."
<p>This data accompanies the paper entitled Allostery and evolution: a molecular journey throught the structural and dynamical landscape of an enzyme super family.</p> <p>The zip archive contains: </p> <p>1- Starting configurations of the proteins after equilibration in PDB format and trajectories of unrestrained molecular dynamics simulations with the positions of the proteins every 100 ps in XTC gromacs format are provided for all systems. </p> <p>2- The free energy profiles and histograms are provided for all umbrella sampling simulations and the scripts used to run it with gromacs.</p>
Advanced Molecular Dynamics Model for Investigating Biological-Origin Microfibril Structures
<p>This data contains all necessary input file to construct the micro fibril.</p>
Dataset- Unraveling the Molecular Complexity of N-Terminus Huntingtin Oligomers: Insights into Polymorphic Structures
<p>This dataset contains self-assembly simulations of oligomeric huntingtin with varying polyQ lengths, related to "Unraveling the Molecular Complexity of N-Terminus Huntingtin Oligomers: Insights into Polymorphic Structures". Peptide systems are of N17+ polyQ, with polyQ adopting lengths between 7 to 45 repeats.</p> <h1></h1>
Data belonging to "Effect of molecular structure on the infrared signaturesof astronomically relevant PAHs"
<p>The data provided here form the basis of the publication titled:</p> <p>"Effect of molecular structure on the infrared signaturesof astronomically relevant PAHs"</p> <p>Which is published in Astronomy and Astrophysics</p> <p>The paper can be downloaded from:</p> <p>https://www.aanda.org/articles/aa/pdf/2019/01/aa34130-18.pdf</p> <p>The data contain raw spectra, both experimental and computational, mass spectrometric data and Cartesian coordinates of the optimized stuctures molecules studied in this work.</p> <p> </p>
Molecular Simulation Elaborating the Structural Mechanism of Spiri forming nitrilase from Bacillus safensis
<p><span>Nitrilases are indispensable in the biocatalytic hydrolysis of nitrile compounds, which presents promising applications in industrial biocatalysis and environmental remediation. In this study, we conduct an extensive investigation into the structural and functional properties of <em>Bacillus safensis </em>nitrilase (<em>BsNIT</em>), highlighting its assembly, substrate binding mechanisms, stability, evolutionary relationships, and active site conservation. Using a combination of molecular modeling and extensive molecular dynamics simulations, we unveil the intricate architecture of <em>BsNIT</em>, which exhibits a left-handed spiri-forming structure stabilized by interchain interactions and salt-bridge formations. The substrate-binding pocket, surrounded by aromatic residues, displays multifaceted accessibility through distinct channels. Our simulations reveal substrate-specific catalytic orientations, with glutaronitrile and 4-cyanobutanoic acid displaying stable binding, while benzonitrile exhibits a propensity for rapid product diffusion. Analysis of active site conservation emphasizes the functional significance of preserved catalytic residues, providing insights into <em>BsNIT</em>'s catalytic efficiency. This comprehensive study offers a thorough understanding of <em>BsNIT</em>'s structure-function relationships, paving the way for future advancements in enzyme engineering and bioremediation strategies targeting nitrile pollutants.</span></p>
The molecular architecture of the desmosomal outer dense plaque by integrative structural modeling
<p>This record pertains to the integrative model of the desmosome ODP based on data from X-ray crystallography, electron cryo-tomography, immuno-electron microscopy, yeast two-hybrid experiments, co-immunoprecipitation, in vitro overlay, in vivo co-localization assays, in-silico sequence-based predictions of transmembrane and disordered regions, homology modeling, and stereochemistry information. The modeling was performed using Bayesian integrative structure determination via IMP (Integrative Modeling Platform).</p> <p>This record contains a) compressed version of Github folder: input data, scripts for modeling and results including bead models and localization probability density maps,and b) the ensemble of major cluster models for the main and supplementary runs reported in the paper.</p>
Coarse-Grained and Multi-Dimensional Data-Driven Molecular Generation: A Structure-Based Framework for Selective Inhibitor Design and Optimization
<p><span>Many approaches not only fail to consider the intricate binding pocket interactions, leading to molecules with suboptimal properties and stability, but also struggle with designing selective inhibitors. To address this challenge, we have developed an innovative structure-based three-dimensional molecular generation framework named </span><span>Coarse-grained and Multi-dimensional Data-driven molecular generation (CMD-GEN). This framework bridges three-dimensional ligand-protein complex data with two-dimensional drug-like molecule data by utilizing coarse-grained pharmacophore points sampled from diffusion models, thereby enriching the training data for generative models.</span> <span>Through a hierarchical architecture, it decomposes the generation of three-dimensional molecules within the pocket into sampling of coarse-grained pharmacophore points, generating of chemical structures, and alignment of conformations, avoiding the instability issues associated with inherent in deep generative model-based generation of molecular conformations.<br><br>This project provide the source dataset used to train and evaluate the overall model.<br></span></p>
Molecular structure discovery for untargeted metabolomics using biotransformation rules and global molecular networking
<p>Comparative analysis of SIRIUS to evaluate our method, Biotransformation-based Annotation Method (BAM). This dataset includes all scripts, data, and results relevant to this analysis. BAM can be found on GitHub (https://github.com/HassounLab/BAM). </p> <p> </p> <p> </p>
Supplementary Data for "Molecular dynamics simulations provide structural insight into binding of cyclic dinucleotides to human STING protein"
<p>Supplementary Data for "Molecular dynamics simulations provide structural insight into binding of cyclic dinucleotides to human STING protein", Journal of Biomolecular Structure and Dynamics, 2021, 10.1080/07391102.2021.1942213</p> <p>A random selection of 10 representative structures from each MSM state of STING/CDN complexes is provided in .pdb file format. The selected MSM representatives are aligned and available as PyMOL session files.</p>
Structures for "Protonation States of Molecular Groups in the Chromophore-Binding Site Modulate Properties of the Reversibly Switchable Fluorescent Protein rsEGFP2"
<p>Files with atomic coordinates of the structures obtained in geometry optimization of molecular systems within the protein and cluster models. Supplementary materials for the paper "Protonation States of Molecular Groups in the Chromophore-Binding Site Modulate Properties of the Reversibly Switchable Fluorescent Protein rsEGFP2"</p>
Dataset for "Structural and molecular indices in common carp (Cyprinus carpio L.) fed n-3 PUFA enriched diet. Food and Chemical Toxicology, 151, 112146."
<p>Dataset for "<strong><em>Eljasik P, Panicz R, Sobczak M, Sadowski J, Tórz A, Barbosa V, Marques A, Dias J. (2021). </em></strong><em>Structural and molecular indices in common carp (Cyprinus carpio L.) fed n-3 PUFA enriched diet. </em><strong><em>Food and Chemical Toxicology, 151, 112146. </em></strong><em>DOI: <a href="https://www.sciencedirect.com/science/article/abs/pii/S0278691521001794?via%3Dihub">doi.org/10.1016/j.fct.2021.112146</a>"</em></p>
Nanoporous carbon structures of different densities generated through GAP molecular dynamics
<p>These nanoporous (NP) carbon atomic structures, in extendend XYZ format, have been generated using a melt-graphitization-quench molecular dynamics (MD) protocol using a Gaussian interatomic potential (GAP) for amorphous carbon [1]. Simulation details and characterization of structural and mechanical properties will follow shortly in a scientific paper.</p> <p><strong>References</strong></p> <p>[1] M.A. Caro. GAP interatomic potential for amorphous carbon (2.0) [Data set]. Zenodo, 10.5281/zenodo.5243184 (2021).</p>
Structural determinants of ligands recognition by the human mitochondrial basic amino acids transporter SLC25A29. Insights from molecular dynamics simulations of the c-state.
<p>Initial coordinates, molecular dynamics trajectories and representative snapshots resulting from the study "Structural determinants of ligands recognition by the human mitochondrial basic amino acids transporter SLC25A29. Insights from molecular dynamics simulations of the c-state." by Pasquadibisceglie and Polticelli.</p> <p>The MD folders contain the parameter/topology (parm7) and initial coordinates (rst7) for the molecular dynamics simulations. Moreover, a NetCDF trajectory "prod.nc" of the production phase is also included.<br> In detail:<br> - MD0 -> SLC25A29 in absence of ligands;<br> - MD1, MD3, MD4 -> SLC25A29-ARG complex;<br> - MD1-LYS, MD3-LYS, MD4-LYS -> SLC25A29-LYS complex.</p> <p>The folder PDB_figures contains the PDB files used to produce the figures presented in the manuscript.</p>
Spliced isoforms of the cardiac Nav1.5 channel modify channel activation by distinct structural mechanisms: Molecular dynamics coordinate and trajectory files
<p>Molecular dynamics files associated with the publication: Spliced isoforms of the cardiac Nav1.5 channel modify channel activation by distinct structural mechanisms</p>
Molecular dynamics simulations in: High-resolution structures with bound Mn2+ and Cd2+ map the metal import pathway in an Nramp transporter
<p>Transporters of the Nramp (Natural resistance-associated macrophage protein) family import divalent transition metal ions into cells of most organisms. By supporting metal homeostasis, Nramps prevent disorders related to metal insufficiency or overload. Previous studies revealed that Nramps take on a LeuT fold and identified the metal-binding site. We present high- resolution structures of <em>Deinococcus radiodurans</em> Nramp in three stable conformations of the transport cycle revealing that global conformational changes are supported by distinct coordination geometries of its physiological substrate, Mn2+, across conformations and conserved networks of polar residues lining the inner and outer gates. A Cd2+-bound structure highlights differences in coordination geometry for Mn2+ and Cd2+. Measurements of metal binding using isothermal titration calorimetry indicate that the thermodynamic landscape for binding and transporting physiological metals like Mn2+ is different and more robust to perturbation than for transporting the toxic Cd2+ metal.</p>
Molecular modeling of self-assembling peptides MELD structures
<p>Top 10 MELD structures for each system used in the "Molecular modeling of self-assembling peptides" paper.</p>
ConforMine Molecular Dynamics Data: Conformational Variability, Secondary Structure Propensities and Molecular Dynamics Simulations
<pre>This dataset contains all the data used to calculate Conformational Variability (ConVa) and Conformational Propensities as well as to train ConforMine. Each directory one level below this document contains another readme for further explanation on the contained data. The following information can be found in this dataset: </pre> <ul> <li>ConforMine_MD_training_sequences.fasta: FASTA file with the amino acid sequences of all used proteins.</li> <li>simulations (directory): Contains all the raw data derived from the MD simulations.</li> <li>ConforMine_training_MD_dihedrals (directory): Contains .xvg files with the dihedral angles of each amino acid at each step of the MD simulation.</li> <li>ConforMine_training_data_conformational_variability (directory): Contains the Conformational Variability values for all amino acids. Each file contains all ConVa values for a whole protein. The data is provided in .csv and .npy format.</li> <li>ConforMine_training_data_conformational_propensities (directory): Contains the Conformational Propensities values for all amino acids. Each file contains all propensities for a whole protein. The data is provided in .csv and .npy format.</li> </ul>
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.