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347 results for “structural proteins”
HerpesFolds: A proteome-wide structural systems approach reveals insights into protein families and activities of all nine human herpesviruses
<p>These are the AlphaFold output files and ChimeraX sessions for "HerpesFolds: A proteome-wide structural systems approach reveals insights into protein families and activities of all nine human herpesviruses" by Timothy K. Soh, Sofia Ognibene, Saskia Sanders, Robin Schäper, Benedikt B. Kaufer, and Jens B. Bosse.</p>
Protein structure data for "AI-predicted protein deformation encodes energy landscape perturbation"
<p>AF2-predicted protein structures of WT and mutant proteins that have corresponding ddG measurements in the ThermoMutDB database of protein mutant stability measurements. PDB structures are compressed using <a href="https://github.com/steineggerlab/foldcomp/">FoldComp</a>, and saved in "structures.zip".</p> <p>Summary of the final dataset and results can be found in "results_summary.pkl".</p> <p>Code used to plot figures can be found in "code4figs.zip".</p>
Body temperature protein X-ray crystallography at 37°C: A rhenium protein complex seeking a physiological condition structure: Raw Diffraction Images (112 week soak) Zenodo
<p>The labratory dataset of the raw diffraction images obtained after 112 weeks of soaking in the mother liquor and collected at a wavelength of 1.54 Å, illustrating the covalent coordination of the rhenium(I) tricarbonyl fragment to the His and Asp amino acid residues as well as other similarities when comparing the 37°C data set to 100K data set as described in the publication titled "Body temperature protein X-ray crystallography at 37°C: A rhenium protein complex seeking a physiological condition structure", written by Jacobs, Helliwell & Brink,<em> ChemComm</em>, 2024.</p> <p>The raw diffraction images for the labratory data sets are made available at the Zenodo research data archive, as specified in the publication.</p>
Supporting data for "Reengineering of a Carotenoid-binding Protein Based on NMR Structure"
<p>List of PDB codes used for MPNN benchmarking, parameters for AXT simulations, molecular dynamics trajectories and domain swapping predictions.</p>
Input files for MD simulations of VP40 matrix protein dimer-dimer structure for WT, G198R, and G201R
<p>For AA simulations, the inp files need to have the path for the toppar folder and the corresponding pdb/psf files need to be renamed.</p>
Data table 3 from publication "Impaired interactions of ataxin-3 with protein complexes reveals their specific structure and functions in SCA3 Ki150 model" (doi.org/10.3389/fnmol.2023.1122308)
Open the record for dataset details and reuse information.
Structural studies of the IFNλ4 receptor complex using cryoEM enabled by protein engineering
<p>MD trajectories for use with the analysis code in https://github.com/bylehn/ifnl4-structure-paper</p>
Exploring zero-shot structure-based protein fitness prediction
<p>This repository contains data used in Exploring zero-shot structure-based protein fitness<br>prediction.</p> <p>Directions to use this data can be found on <a href="https://github.com/gitter-lab/benchmarking-structure-based-models">our GitHub repository</a>.</p> <ol> <li><code>experimental_struct_artifacts</code> contains the experimentally determined structures for ProteinGym assays used in our analysis along with the reference file needed to generate ESM inverse folding predictions for these structures in ProteinGym.</li> <li><code>results</code> contains the prediction results obtained by running SSEmb on the 216 ProteinGym assays being considered in this study.</li> <li><code>test.tar.gz</code> contains all the structures from ProteinGym as well as MSAs generated using mmseqs2. To use this directory: <ul> <li>Setup SSEmb as directed in its <a href="https://github.com/KULL-Centre/_2023_Blaabjerg_SSEmb">repository</a></li> <li>Download this file and extract it in the data folder.</li> </ul> </li> </ol> <p> </p> <p> </p>
Predicted structures of the periplasmic adaptor protein, CmeA
<p>Predicted structures for CmeA, sequence alignments, and a fully assembled model for CmeABC (Chapter 6 of Kahlan Newman's Doctoral Thesis). </p>
Protein preparation (1LPB), docked structures of Bromhexine and Orlistat to Pancreatic Lipase, and MD simulations trajectories in 3 replicas.
<p>Data set contains 3 folders:</p> <p>1) Protein preparation (1LPB)</p> <p>2) XP Docking of Bromhexine and Orlistat</p> <p>3) MD Simulation of Bromhexine and Orlistat (3 replicates)</p>
Exploring the Chemical Space of Glycosylation in Noncovalent Protein Complexes: an Expedition along Different Structural Levels of Human Chorionic Gonadotropin Employing Mass Spectrometry
<p><strong>Supplementary files for "Exploring the Chemical Space of Glycosylation in Noncovalent Protein Complexes: an Expedition along Different Structural Levels of Human Chorionic Gonadotropin Employing Mass Spectrometry"</strong></p> <p><strong>Introduction</strong></p> <p>This data repository contains all previously unpublished raw data files for the manuscript “Exploring the Chemical Space of Glycosylation in Noncovalent Protein Complexes: an Expedition along Different Structural Levels of Human Chorionic Gonadotropin Employing Mass Spectrometry” by Maximilian Lebede<sup>||</sup>, Fiammetta Di Marco<sup>||</sup>, Wolfgang Esser-Skala, René Hennig, Therese Wohlschlager, Christian G. Huber.</p> <p><strong>Files</strong></p> <p>This repository contains 9 files:</p> <ul> <li><strong>Dimer Raw Files.zip</strong> folder containing 4 files of native-MS data (*.raw, Thermo RAW file format) of two batches of the drug product Ovitrelle® at native dimer level. </li> <li><strong>H11M9 Ovitrelle BA056714 Glycopeptide R1 230920_07.zip</strong> folder containing 1 file of HPLC-MS/MS glycopeptide data (*.raw, Thermo RAW file format) of one batch of the drug product Ovitrelle®.</li> <li><strong>H11M9 Ovitrelle BA056714 Glycopeptide R2 230920_08.zip</strong> folder containing 1 file of HPLC-MS/MS glycopeptide data (*.raw, Thermo RAW file format) of one batch of the drug product Ovitrelle®.</li> <li><strong>H11M9 Ovitrelle BA056714 Glycopeptide R3 230920_09.zip</strong> folder containing 1 file of HPLC-MS/MS glycopeptide data (*.raw, Thermo RAW file format) of one batch of the drug product Ovitrelle®.</li> <li><strong>H11M9 Ovitrelle BA059433 Glycopeptide R1 240920_15.zip</strong> folder containing 1 file of HPLC-MS/MS glycopeptide data (*.raw, Thermo RAW file format) of one batch of the drug product Ovitrelle®.</li> <li><strong>H11M9 Ovitrelle BA059433 Glycopeptide R2 240920_16.zip</strong> folder containing 1 file of HPLC-MS/MS glycopeptide data (*.raw, Thermo RAW file format) of one batch of the drug product Ovitrelle®.</li> <li><strong>H11M9 Ovitrelle BA059433 Glycopeptide R3 240920_17.zip</strong> folder containing 1 file of HPLC-MS/MS glycopeptide data (*.raw, Thermo RAW file format) of one batch of the drug product Ovitrelle®.</li> <li><strong>MoFi Settings.zip</strong> folder containing 12 files of MoFi settings (*.xml) to annotate deconvoluted spectra of hCG subunits and dimer of two Ovitrelle® batches, untreated and after desialylation. A typical MoFi setting file is build from protein sequence (*.FASTA), monosaccharide and frequent modification atomic composition (*.csv), glycan or glycoform library (*.csv) and deconvoluted spectrum in centroid (*.csv). Files are named as following: Settings_Ovitrelle_Batch number (BA056714 or BA059433)_Structural level (Alpha, Beta or Dimer)_Enzymatic treatement (Untreated or Sialidase).</li> <li><strong>Subunit Raw Files.zip</strong> folder containing 8 files of HPLC-MS data (*.raw, Thermo RAW file format) of two batches of the drug product Ovitrelle® at intact subunit level. </li> </ul> <p>Raw files are named as following: Instrument, Drug product (Ovitrelle), Batch number (BA056714 or BA059433), Structural level (Dimer, Subunits or Glycopeptides), Enzymatic treatment (untreated, Sialidase, PNGase F or PNGase F + Sialidase) and date. Glycopeptide data includes 3 replicates (R1-3).</p> <p><strong>License</strong></p> <p>This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit <a href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</a> .</p> <p> </p>
MD data for "Selective G protein signaling driven by Substance P-Neurokinin Receptor structural dynamics"
<p>Molecular dynamics (MD) data for "Selective G protein signaling driven by Substance P-Neurokinin Receptor structural dynamics" (Harris <em>et al.</em>, Nature Chemical Biology (2021), DOI: 10.1038/s41589-021-00890-8, URL: https://www.nature.com/articles/s41589-021-00890-8). See the included readme.txt for more details. Please cite the paper if you use these data.</p>
Structure, Function and Dynamics in Acyl Carrier Proteins.
<p><strong>Original Article: </strong>https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0219435</p> <p><strong>Primary GitHub Repository:</strong> https://github.com/rohitfarmer/acp-dynamics</p> <p><strong>Folders</strong></p> <ul> <li><strong>Figures:</strong> Coordinates (.pdb) for structures used in figure panels. The number in the file name denotes the frame number in the simulation. Each frame was captured at 10 ps therefore frame number 100 would mean 100 X 10 = 1000 ps = 1 ns. <a href="https://pymolwiki.org/index.php/Linux_Install">Pymol</a> session files (.pse), and <a href="https://inkscape.org/">Inkscape</a> files (.svg) that were used to generate the figures are also provided.</li> <li><strong>Scripts:</strong> Perl scripts used in the project.</li> <li><strong>Simulations:</strong> Simulations are in compressed .pdb.zip format with the labelling corresponding to Table 1 in the main paper. To comply with the size allowance of GitHub, GROMACS trajectories that were initially recorded at 10 ps time intervals are reduced to 100 ps time intervals for 200 ns simulations and to 500 ps time intervals for 1 microsecond simulations. Trajectories are converted to PDB format with no water molecules and ions and compressed to individual zip files. Uncompressed simulation files can be visualized in <a href="https://www.ks.uiuc.edu/Research/vmd/">VMD</a>. <ul> <li><strong>amber99sb-ildn.ff:</strong> Amber 99 SB ILDN force field with added parameters from GAFF.</li> </ul> </li> </ul>
Figure 6 in A novel epidermal gland type in lizards (α-gland): structural organization, histochemistry, protein profile and phylogenetic origins
Figure 6. Transmission electron microscopy of the epithelium from the femoral area of Tropidurus catalanensis. A, general view of the glandular epithelium showing major skin layers and abundance of vesicles inside glandular cells. B–G, magnified view of glandular tissue showing: B, clusters of melanin granules and numerous vesicles; C, aggregations of four different types of vesicles (V1, V2, V3 and V4); D, E, Golgi apparatuses amid secretory vesicles; F, autophagocytic events (arrowheads indicate membrane projections); G, iridophores present in the apical portion of the dermis. Legend: Go, Golgi complex; Ir, iridophore; Me, melanin granule; Nu, nucleus; V1, vesicles type 1; V2, vesicles type 2; V3, vesicles type 3; V4, vesicles type 4.
Figure 3 in A novel epidermal gland type in lizards (α-gland): structural organization, histochemistry, protein profile and phylogenetic origins
Figure 3. Maderson & Chiu's (1970) model of epidermal gland evolution. Steps of the model are briefly described in items A–G.
Figure 2 in A novel epidermal gland type in lizards (α-gland): structural organization, histochemistry, protein profile and phylogenetic origins
Figure 2. Histological structure of unspecialized skin and epidermal glands. Diagrammatic representation of the unspecialized squamate skin and major epidermal gland types, illustrating their respective secretion mechanisms as hypothesized by Maderson (1972).
Figure 5. A in A novel epidermal gland type in lizards (α-gland): structural organization, histochemistry, protein profile and phylogenetic origins
Figure 5. A, unspecialized scales from the pre-cloacal flap of a male Stenocercus caducus (MZUSP-R 82815). B, unspecialized scales from the femoral area of a female Tropidurus chromatops (MZUSP-R 106266). C, scales with α-glands from the femoral area of male T. chromatops (MZUSP-R 106263). Note that β-keratin layers are not present in A and C because they were lost during sample preparation. D, unspecialized scale (stage I) from the humeral region of a female T. chromatops (MZUSP-R 106266). E, detail of a scale with α-gland (stage IV) from the femoral area of a male T. xanthochilus (MZUSP-R 106342). F, detail of a scale with α-gland (stage V) from the pre-cloacal flap of a male T. xanthochilus (MZUSP-R 106342). G, detail of a scale with α-gland (stage VI) from the femoral areal of a male T. xanthochilus (MZUSP-R 106336). H, part of the inner generation of an α-gland from the femoral area of a male Plica plica (MTR 18918) showing the glandular stratum with a large number of secretory vesicles (indicated with an asterisk). I, part of the inner generation of the α-gland from the femoral area of a male T. catalanensis (MZUSP-R 106470) with melanophores transferring melanin granules into glandular cells and numerous melanin granules accumulated in their cytoplasm. J, glandular tissue of the outer generation
Figure 9 in A novel epidermal gland type in lizards (α-gland): structural organization, histochemistry, protein profile and phylogenetic origins
Figure 9. Ancestral state reconstructions of α-gland/flash mark related characters of tropidurid lizards.
Figure 4 in A novel epidermal gland type in lizards (α-gland): structural organization, histochemistry, protein profile and phylogenetic origins
Figure 4. Ventral view of (A) a male Tropidurus chromatops Harvey & Gutberlet, 1998 (MHNC-R 3018) from ~30 km W Florida, Santa Cruz, Bolivia, (B) a male T. melanopleurus Boulenger, 1902 (IBIGEO-R 5331) from Aguas Blancas, Salta, Argentina, (C) a female T. xanthochilus Harvey & Gutberlet, 1998 (MZUSP-R 106321) from Santo Antônio do Leverger, Mato Grosso, Brazil, and (D) a male T. etheridgei Cei, 1982 (AMNH-R 176273) from Filadelfia, Boquerón, Paraguay, illustrating the location and coloration of flash marks observed (or not) on the ventral body of tropidurines. Black squares in (A) indicate body areas from which we collected skin samples for histological examination. In (D) the yellow coloration covering the background of the black flash-marks of T. etheridgei might either represent a transient ontogenetic state or an instance in which a yellow background persists throughout life.
Atomic-Resolution Structure of the Protein Encoded by Gene V of fd Bacteriophage in Complex with Viral ssDNA Determined by Magic-Angle Spinning Solid-State NMR
<p>F-specific filamentous phages, elongated particles with circular single-stranded DNA encased in a symmetric protein capsid, undergo an intermediate step, where thousands of homodimers of a non-structural protein, gVp, bind to newly synthesized strands of DNA, preventing further DNA replication and preparing the circular genome in an elongated conformation for assembly of a new virion structure at the membrane. While the structure of the free homodimer is known, the ssDNA-bound conformation has yet to be determined. We report an atomic-resolution structure of the gVp monomer bound to ssDNA of fd phage in the nucleoprotein complex elucidated via Magic-Angle Spinning solid-state NMR. The model presents significant conformational changes with respect to the free form. These modifications facilitate the binding mechanism and possibly promote cooperative binding in the assembly of the gVp-ssDNA complex.</p> <p>The raw NMR data used for structure determination are uploaded as original Bruker directories from topspin version 3.5. Processing details are given in the supporting Information of the manuscript. PDB ID is 8ACZ. BMRB accession number is 51391.</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.