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289 results for “Molecular structure”
Supporting data for: Condensed-phase molecular representation to link structure and thermodynamics in molecular dynamics
<p>This repository contains supporting data and code for the paper titled "Condensed-phase molecular representation to link structure and thermodynamics in molecular dynamics" by Bernadette Mohr, Diego van der Mast, and Tristan Bereau.</p>
Data for manuscript "Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting"
<p>The tar file contains the input files for RADICAL augmented MDFF implementation (R-MDFF) for two protein systems, Adenylate Kinase (ADK) and Carbon Monoxide Dehydrogenase (CODH). These examples demonstrate the implementation of R-MDFF using RADICAL-Cybertools to flexibly fit biomolecules in cryo-EM density maps with on-the-fly decision making.</p> <p>All molecular simulations were performed using CUDA enabled NAMD 2.14 installed on OLCF Summit HPC resource. The CHARMM36 force field parameters were used for the proteins. Synthetic density maps were prepared at 1.8, 3 and 5 Å for ADK and 1.8 and 3 Å for CODH using VMD 1.9.3 software installed on OLCF Summit HPC resource. During the analysis stage, the cross correlation coefficients between density maps and atomic model were computed using VMD 1.9.3 on Summit HPC as part of the R-MDFF workflow.</p> <p>The source code is publicly available on GitHub: <a href="https://github.com/radical-collaboration/MDFF-EnTK">https://github.com/radical-collaboration/MDFF-EnTK </a></p> <p>The preprint of this research is submitted on bioRxiv, doi: <a href="https://doi.org/10.1101/2021.12.07.471672">https://doi.org/10.1101/2021.12.07.471672 </a></p> <p>To obtain maximum compression of the data, the tar command used to generate this tarball was:</p> <pre><code class="language-bash">GZIP=-9 tar --exclude='last.pdb' --exclude='*last_from_prev_iter.pdb' --exclude='*old' --exclude='*log' --exclude='*coor' --exclude='*vel' --exclude='*xsc' --exclude='*dcd' --exclude='lastframepdbs_fix' --exclude='*out' --exclude='*sl' --exclude='*rs' --exclude='*prof' --exclude='*err' --exclude='*dx' --exclude='*grid.pdb' --exclude='*txt' -cvzf rmdffv2.tar.gz rmdff-zenodo/</code></pre> <p> </p>
Molecular Models obtained in the paper "In situ architecture of the ER-mitochondria encounter structure"
<p>The zip file contains prototypical NAMD input files to carry out the molecular dynamics flexible fitting simulations performed in the paper, and the initial and final structures (best models) obtained using the MDFF protocol.</p>
Protein Structure Files and Galaxy Workflows for Conducting Molecular Dynamics Simulations of Flavivirus Helicases -- Output Files
<p>These are the output files generated using the input files and Galaxy workflows for flavivirus helicase simulations, from: </p> <pre>https://doi.org/10.5281/zenodo.7493015</pre>
Dual structure of a vanadyl-based molecular qubit containing a bis(β-diketonato) ligand. Open dataset
<p>Data supporting the original figures 2, 4, 6, and 7 of the related publication</p>
Pleiotropic effects of trisomy and pharmacologic modulation on structural, functional, molecular, and genetic systems in a Down syndrome mouse model
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Data from: Chemical structure predicts the effect of plant-derived low-molecular weight compounds on soil microbiome structure and pathogen suppression
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Arthropod food webs in the foreland of a retreating Greenland glacier: Integrating molecular gut content analysis with Structural Equation Modelling
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Molecular dynamics simulations in: High-resolution structures with bound Mn2+ and Cd2+ map the metal import pathway in an Nramp transporter
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Supplementary material 1 from: Grabowska J, Kvach Yu, Rewicz T, Pupins M, Kutsokon I, Dykyy I, Antal L, Zięba G, Rakauskas V, Trichkova T, Čeirāns A, Grabowski M (2020) First insights into the molecular population structure and origins of the invasive Chinese sleeper, Perccottus glenii, in Europe. NeoBiota 57: 87-107. https://doi.org/10.3897/neobiota.57.48958
Table S1. Table presents Chinese sleeper haplotypes frequency (belonging to three distinguished groups) found in studies sites.
Data from: Polygamy and an absence of fine-scale structure in Dendroctonus ponderosae (Hopk.) (Coleoptera: Curcilionidae) confirmed using molecular markers
An understanding of mating systems and fine-scale spatial genetic structure is required to effectively manage forest pest species such as Dendroctonus ponderosae (mountain pine beetle). Here we used genome-wide single-nucleotide polymorphisms to assess the fine-scale genetic structure and mating system of D. ponderosae collected from a single stand in Alberta, Canada. Fine-scale spatial genetic structure was absent within the stand and the majority of genetic variation was best explained at the individual level. Relatedness estimates support previous reports of pre-emergence mating. Parentage assignment tests indicate that a polygamous mating system better explains the relationships among individuals within a gallery than the previously reported female monogamous/male polygynous system. Furthermore, there is some evidence to suggest that females may exploit the galleries of other females, at least under epidemic conditions. Our results suggest that current management models are likely to be effective across large geographic areas based on the absence of fine-scale genetic structure.
FIGURES 1–9. 1–3. Philophylla millei, n in A new species of Philophylla Rondani (Diptera: Tephritidae: Trypetini) from New Caledonia, recognized based on female postabdominal structure and molecular sequence data
FIGURES 1–9. 1–3. Philophylla millei, n. sp., holotype male. 4. P. millei, n. sp., paratype female. 5. Anastrephoides matsumurai Shiraki, female. 6. Myoleja korneyevi Han & Kütük, female. 7. M. korneyevi, male. 8. Anastrepha barnesi Aldrich. 9. Anastrepha obliqua (Macquart). Abbreviations: AAB = anterior apical band; PAB = posterior apical band; RMB = radial-medial band; SAB = subapical band; SCB = subcostal band.
FIGURE 16 in A new species of Philophylla Rondani (Diptera: Tephritidae: Trypetini) from New Caledonia, recognized based on female postabdominal structure and molecular sequence data
FIGURE 16. Relationships of the tribe Trypetini inferred from neighbor-joining tree based on Kimura two parameter distances (1159 bp after gaps and sites with missing data removed). The first number is the Pc value from the standard error test (higher than 90%), and the second number is the Pb from the bootstrap test (2000 replications).
FIGURE 10–15 in A new species of Philophylla Rondani (Diptera: Tephritidae: Trypetini) from New Caledonia, recognized based on female postabdominal structure and molecular sequence data
FIGURE 10–15. Philophylla millei, sp.n.; 10. epandrium and surstyli, posterior view (proctiger removed); 11. epandrium, surstyli, and proctiger, lateral view; 12. glans, dorsolateral view (inset at 8x main figure); 13. female postabdomen, ventral and dorsal views (insets at 8x main figures); 14. spermatheca; 15. aculeus, ventral and dorsolateral views.
DrugMol3D: An Expanded Collection of Molecular Data for Optimized Drug Structures and Descriptive Properties
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MD data for the article "Structure comparison of beta amyloid peptide Aβ 1-42 isoforms. Molecular dynamics modeling" by Anna P. Tolstova, Alexander A. Makarov, Alexei A. Adzhubei.
<p>There are CMD and REMD trajectories for Aβ isoforms discussed in the paper together with final coordinate files for these trajectories. The resulting dataset of modeled structures includes wild type Aβ42, isoD7, pS8, D7H and H6R-Aβ42, and wild type Aβ16, isoD7, pS8, D7H and H6R-Aβ16.</p>
Identification of Potential IL4I1 Inhibitors through Structure-Based Virtual Screening and Molecular Dynamics Simulations, Molecular dynamics trajectory file
<p>Dataset for molecular dynamics simulations of the article: Identification of Potential IL4I1 Inhibitors through Structure-Based Virtual Screening and Molecular Dynamics Simulations.</p> <p><a href="../api/records/10473570/draft/files/First_600ns_MD.rar/content" target="_blank" rel="noopener noreferrer">First_600ns_MD.rar</a> contains the 600ns molecular dynamics simulation trajectory file of IL4I1-FAD-CIT complex using desmond.</p> <p><a href="../api/records/10473570/draft/files/Second_500ns_MD_ZL35_F963.rar/content" target="_blank" rel="noopener">Second_500ns_MD_ZL35_F963.rar </a>contains the 500ns molecular dynamics simulation trajectory file of IL4I1-FAD-ZL35 complex, which initial conformation of this part of dynamics simulation was obtained by docking the conformation of the 963rd frame from the first dynamics simulation with ZL35 through induced fit.</p> <p>script.rar include scripts and calculation methods for free energy landscape, RMSD matrix, and thermol MM/GBSA.</p>
Perpendicular Crossing Chains Enable High Mobility in a Non-Crystalline Conjugated Polymer: Molecular Dynamics Forcefields and Structures
<p>This repository contains molecular dynamics forcefields and structures used to produce results described in the research article: "<em>Perpendicular Crossing Chains Enable High Mobility in a Non-Crystalline Conjugated Polymer</em>" published in <em>Proceedings of the National Academy of Sciences</em> (DOI:10.1073/pnas.2403879121)</p> <p>The following data is available:</p> <ul> <li>Coarse-grained forcefields of the conjugated polymer C16-IDTBT (12mer and 24mer).</li> <li>Coarse-grained structures of single chains of C16-IDTBT (12mer and 24mer).</li> <li>Atomistic forcefields of the conjugated polymer C16-IDTBT (12mer and 24mer).</li> <li>Atomistic structures of single chains of C16-IDTBT (12mer and 24mer).</li> <li>Bonded and non-bonded parameter files for the atomistic C16-IDTBT forcefields.</li> <li>Coarse-grained structures of thin film models (1 x C16-IDTBT 24mers, 3 x C16-IDTBT 12mers, 3 x P3HT 48mers, 3 x PffBT4T-2OD 12mers).</li> <li>Backmapped (atomistic) structures of thin film models (1 x C16-IDTBT 24mers, 3 x C16-IDTBT 12mers, 3 x P3HT 48mers, 3 x PffBT4T-2OD 12mers).</li> </ul> <p>Coarse-grained models are based on the Martini 3 forcefield: Souza, P. et al., <em>Nature Methods</em>, 2021, (https://doi.org/10.1038/s41592-021-01098-3). The bonded and nonbonded parameters may be sourced from the Martini website: https://cgmartini.nl/</p> <p>Atomistic models are based on the OPLS-AA forcefield: Kaminski, G. A. et al.,<em> J. Phys. Chem. B</em>, 2001, (https://doi.org/10.1021/jp003919d). The required bonded and nonbonded parameters have been included in this repository for convenience.</p> <p>Please note that the C16-IDTBT atomistic forcefields and single chain structures have previously been published in another repository (https://doi.org/10.11583/DTU.c.5254236.v1). They are included here for completeness.</p> <p>For any further data related to this research article, please contact the authors.</p>
Molecular dynamics simulations reveal the selectivity mechanism of structurally similar agonists to TLR7 and TLR8
<p>Trajectory, topology and index files for TLR7 (apo), TLR7-R, TLR7-H, TLR7-G, TLR8 (apo), TLR8-R, TLR8-H, TLR8-G systems. </p>
Research Data for "Molecular Dynamics Study of Structure and Reactions at the Hydroxylated Mg(0001)/Bulk Water Interface"
<p>This folder contains data used in the paper "Molecular Dynamics Study of Structure and Reactions at the Hydroxylated Mg(0001)/Bulk Water Interface" (Title subject to change). Some details on the structure are as follows:</p> <p>The folder "figures" contains data to create various figures in the main paper. Each file contains a json object, where keys "0", "1", etc. refer to the 1st/2nd subplot for a figure. The values are then another json object with the data used to create the relevant plot; the most useful of which is the "data" key which contains the plot data.</p> <p>The folder "md_traj" contains the molecular dynamics trajectory. The file "traj.exyz" is a standard format which can be opened with various software. "traj.json" contains the same information in an in-house format used by the author. The "thermo_data.json" contains various thermodynamics properties over the simulation, such as temperatures and kinetic energies. Units are femtoseconds, Angstrom, electron-volts and Kelvin.</p> <p>The folder "react_traj" contains trajectories in the same formats as "md_traj", but each are limited to time-windows where reactions occurred (so each trajectory will only be hundreds of femtoseconds long at most). The subfolder "full_traj" contains the trajectories with all atoms present, whilst "trimmed_traj" contains trajectories with most atoms removed (the atoms included are those nearest the reaction).We include these "trimmed_traj" files as it is difficult to find the reacting molecules when visualising all atoms in the simulation.</p> <p>The folder "opt_geoms" contains geometries for various structures used in the paper (in *.exyz format). These also contain *.json files; these contain information on how the calculations were carried out in a format used by the author (they are small files primarily included for the benefit of the author).</p> <p> </p> <p> </p>
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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.