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249 results for “pocket”
NMR Data for "Unveiling a Key Catalytic Pocket for the Ruthenium NHC-Catalysed Asymmetric Heteroarene Hydrogenation" (DOI: 10.1039/D1SC06409F)
<p># NMR Data for "Unveiling a Key Catalytic Pocket for the Ruthenium NHC-Catalysed Asymmetric Heteroarene Hydrogenation" (DOI: 10.1039/D1SC06409F)</p> <p>In the following, the original NMR Data for the publication "Unveiling a Key Catalytic Pocket for the Ruthenium NHC-Catalysed Asymmetric Heteroarene Hydrogenation" (DOI: 10.1039/D1SC06409F) is provided. </p> <p>## Experimental methodology and associated data</p> <p>### Dataset 200113.40a</p> <p>Inside an argon filled glovebox, 4.6 mg of **1-A** (5.4 µmol) was dissolved in 0.65 mL THF-d<sub>8</sub> (distilled over sodium/benzophenone and stored over 3 Å molecular sieves), yielding a clear, dark yellow solution. The solution was then transferred into a medium pressure J Young NMR tube and sealed. Subsequently, initial NMR spectra under argon atmosphere were recorded (t = 0 h).</p> <p>Afterwards, 2 bar of H2 pressure were applied to the J Young NMR tube, resulting in a partial H<sub>2</sub> pressure of 1 bar (due to the presence of 1 bar argon). After shaking to dissolve the added H<sub>2</sub>, a slow color change to orange could be observed. The reaction was monitored using 1H NMR (Bruker AV 400, 400 MHz), showing consumption of dissolved H<sub>2</sub> as evidenced by a decrease in intensity for the H<sub>2</sub> signal at δ(1H) = 4.55 ppm. Six hours after the first addition of H<sub>2</sub>, the J Young NMR tube was re-pressurized with 2 bar H<sub>2</sub>, and again after 36 h, shaking the NMR tube regularly to dissolve H<sub>2</sub>. After the third pressurization, no further decrease of dissolved H<sub>2</sub> could be observed.</p> <p>#### NMR experiments and timestamps</p> <p>File name | NMR Experiment | Time stamp / h (relative to H<sub>2</sub> addition)<br> --- | --- | ---<br> 200113.40a.1 | 1H | 0<br> 200113.40a.2 | 1H | 0<br> 200113.40a.3 | 1H | 0.5<br> 200113.40a.4 | 1H | 1<br> 200113.40a.5 | 1H | 2.5<br> 200113.40a.6 | 1H | 2.5<br> 200113.40a.7 | 1H | 5 <br> 200113.40a.8 | 1H COSY-45 | 5<br> 200113.40a.9 | 1H | 6.5<br> 200113.40a.10 | 1H | 22.5<br> 200113.40a.11 | 1H | 30<br> 200113.40a.12 | 1H | 31<br> 200113.40a.13 | 29Si-inept | 31<br> 200113.40a.14 | 1H-29Si HMBC | 31<br> 200113.40a.15 | 1H | 45.5<br> 200113.40a.16 | 1H-29Si HMBC | 45.5<br> 200113.40a.17 | 1H | 55<br> 200113.40a.18 | 1H | 69.5<br> 200113.40a.110 | 1H (larger measurement window) | 22.5<br> 200113.40a.111 | 1H (larger measurement window) | 30<br> 200113.40a.115 | 1H (larger measurement window) | 45.5<br> 200113.40a.117 | 1H (larger measurement window) | 55<br> 200113.40a.118 | 1H (larger measurement window) | 69.5</p> <p>### Dataset 200117.40a</p> <p>69.5 h after the first addition of H<sub>2</sub> no significant changes could be observed in the 1H NMR spectra anymore. At this point, 0.15 mL of a 0.052 M solution of benzofuran in THF-d<sub>8</sub> (7.8 µmol benzofuran, ca. 1.5 equivalents relative to **1-A**) were added to the NMR tube while applying 2 bar of H<sub>2</sub> pressure. No significant color change was observed upon addition of the substrate. Subsequently, the NMR tube was sealed and the reaction was monitored using 1H NMR for an additional 119 h, especially following the hydride signals at δ(1H) = −3.7 ppm and δ(1H) = −3.8 ppm as well as the signals of 2,3-dihydrobenzofuran at δ(1H) = 4.48 ppm and δ(1H) = 3.15 ppm. After 119 h of reaction time, the color of the reaction solution had changed to light orange.</p> <p>#### NMR experiments and timestamps</p> <p>File name | NMR Experiment | Time stamp / h (relative to substrate addition)<br> --- | --- | ---<br> 200117.40a.1 | 1H | 0.5<br> 200117.40a.2 | 1H | 1.5<br> 200117.40a.3 | 1H | 7<br> 200117.40a.4 | 1H | 24<br> 200117.40a.5 | 1H | 24.5 <br> 200117.40a.6 | 1H | 72 <br> 200117.40a.7 | 1H COSY-45 | 72<br> 200117.40a.101 | 1H (larger measurement window) | 0.5<br> 200117.40a.103 | 1H (larger measurement window) | 7<br> 200117.40a.104 | 1H (larger measurement window) | 24</p>
Cipher Machine Pocket Terminal TST APT 60 (Inv. 2017-443T2)
<p>This dataset represents the computed tomography image acquisition of a historical cipher machine from the collection of the Deutsches Museum. It is composed of CT reconstructed image stacks in the DICOM (.dcm) format.<br> It can be imported in any free or propietary CT-Viewer that supports the DICOM standard to generated 2D and 3D imaging.<br> If segmentations/ROIs are availabe, they are uploaded in a seperate image stacks and are a subset of the scanned cipher machine.</p> <p>object details:<br> name: Pocket Terminal TST APT 60<br> Inv.-No. of the Deutsches Museum: 2017-443T2</p> <p>file object details:<br> file format: image/dcm<br> pixel spacing unit: mm<br> X pixel spacing: 0.144<br> Y pixel spacing: 0.144<br> Z pixel spacing: 0.144<br> grid size x: 395<br> grid size y: 534<br> grid size z: 675<br> color depth: 16Bit</p> <p>ownership & image acquisition:<br> project: <a href="https://digital.deutsches-museum.de/en/projects/3d-cipher">3D-Cipher</a><br> collection: <a href="https://digital.deutsches-museum.de">Deutsches Museum</a><br> IP holder: Deutsches Museum<br> license: <a href="https://creativecommons.org/licenses/by/4.0/deed.en">Creative Commons BY-SA 4.0</a><br> scanning facility: <a href="https://www.iis.fraunhofer.de/en/ff/zfp.html">Fraunhofer Development Center X-ray Technology EZRT/Fraunhofer IIS</a><br> scanning device: High Energy CT XXL-CT<br> Funding attribution: <a href="https://www.bmbf.de/bmbf/en">German Federal Ministry of Education and Research</a><br> acknowledgement: <a href="https://www.cryptomuseum.com">CryptoMuseum</a> (as main source for informations about the cipher machines)</p>
Pocket gopher esker-krummholz distance data for Martinelli slope and North of Tvan, 1995.
Two ares of Niwot Ridge were examined for simultaneous occurrences of krummholz and eskers created by Thomomys talpoides (Northern pocket gopher) burrowing, to establish a relationship between snowpack and gopher habitat. The krummholz east and northeast of the Martinelli slope and the krummholz north of T-van were surveyed for the abundance of gopher eskers. Using a tape measure, the minimum and maximum distances of the eskers from the krummholz vegetation were measured, with a value of 0 m indicating that the nearest soil core was immediately adjacent to or actually underlying a branch of the tree. With the use of a compass, both the northernmost and southernmost bearings were measured from the krummholz to the esker. The krummholz were tagged at the northeasternmost point whenever possible for consistency, or the northernmost branches of the leeward side of the tree island. All measurements were taken from the nearest protruberance of the krummholz.
All Atom Molecular Dynamics Simulations of Lopinavir at the Binding Pocket of SARS-CoV2 Main Protease
<p>Data includes all of the trajectories (2000) of classical all-atom molecular dynamics (MD) simulations of lopinavir at the binding pocket of SARS-CoV2 main protease target. In order to decrease the size of the file only protein and ligand trajectories were provided. Simulation has been performed with Desmond. Protein–ligand complexes were obtained by Glide/SP docking program. Complex 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<br> 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 ns production run was performed for the simulations.</p>
Dataset for identification of peptidomimetics and FDA approved drugs binding to novel allosteric pocket of the IRE1 RNase domain.
<p>Input files, protein-peptide and ligand docking datasets, and simulation trajectories, compressed in "rar" format. All calculations performed using the Schrödinger 2020-2 / 2020-3 software (modules Glide, Phase, Desmond). </p> <p>SI includes folders:</p> <p>1- "Peptide" folder contains the best peptide "Docking" complexes and "Pharmacophore" models </p> <p>2-"Quercitrin" folder contains the molecular "Docking", "MMGBSA" calculations, and "MD" simulation</p> <p>3-"Pemetrexed" folder contains the molecular "Docking", "MMGBSA" calculations, and "MD" simulation</p> <p> </p>
Figs 14–17. Maechidiini Burmeister, 1855 features. 14. Maechidius corrosus Waterhouse, 1875, antennal pockets. 15. M. major Blackburn, 1888, same. 16. M. spurius Macleay, 1819 in A revision of the Maechidiini Burmeister, 1855 (Coleoptera: Scarabaeidae: Melolonthinae) from the Indo-Australian transition zone, and the first record of the tribe west of Wallace's Line
Figs 14–17. Maechidiini Burmeister, 1855 features. 14. Maechidius corrosus Waterhouse, 1875, antennal pockets. 15. M. major Blackburn, 1888, same. 16. M. spurius Macleay, 1819, holotype, prosternum and pronotal hypomera, ventral view (BMNH). 17. Same, mesoventrite. Not to scale.
Pockets of Open Cells database
<p>Database of Pockets of Open Cells (POCs) detected in MODIS Terra imagery using the machine learning algorithm here: https://zenodo.org/record/4381994. Includes segemented masks and basic physical properties such as size and area.</p>
Fig. 5 in Systematics of the Smooth-Toothed Pocket Gopher, Thomomys umbrinus, in the Mexican Transvolcanic Belt
Fig. 5. Clustering of 12 populations of Thomomys umbrinus along the Mexican Transvolcanic Belt, according to sex (♀♀/33) and age (2, 3). Arrows show the comparisons of the phenograms using Mantel's Z tests (r = correlation; p = significance). Cophenetic coefficients are r = 0.8728 in ♀2; r = 0.8345 in ♀3; r = 0.9150 in 32; r = 0.8062 in 33.
Fig. 4 in Systematics of the Smooth-Toothed Pocket Gopher, Thomomys umbrinus, in the Mexican Transvolcanic Belt
Fig. 4. Distribution of populations of Thomomys umbrinus along the Mexican Transvolcanic Belt in multivariate space, according to sex (♀/3) and age (2–4). Notice that Thomomys umbrinus pullus, when present, always separated from other samples and that the position of the samples is variable in each sex and age. Axes and spheres indicate the position of group localities with respect to Principal Components Analyses computed on the population means. Lines connecting group localities result from a Minimum Spanning Tree projected onto the first principal components (I-III). Percentages refer to the amount of variation explained by each principal component. Discontinuous lines indicate groups according to Cluster Analyses developed in the sample means (r = cophenetic coefficient for the phenograms; n = sample size). Mantel's Z tests (r = correlation; p = significance) and arrows indicate comparability between phenograms. See names of group localities (letters) in table 1. Diagrams were drawn with the same scale and are rotated to different degrees for the sake of clarity.
Fig. 1 in Systematics of the Smooth-Toothed Pocket Gopher, Thomomys umbrinus, in the Mexican Transvolcanic Belt
Fig. 1. Cranial measurements (33) taken in 1145 Thomomys umbrinus from 72 localities in the Mexican Transvolcanic Belt. A, a: dorsal view; B, b: ventral view; C, c: lateral view. See pp. 13 – 15 for explanations of measurements.
Fig. 2 in Systematics of the Smooth-Toothed Pocket Gopher, Thomomys umbrinus, in the Mexican Transvolcanic Belt
Fig. 2. Group localities (GL's) analyzed in the geographic variation of Thomomys dots signal sample localities according to specimens examined in text. Circling lines
Fig. 7 in A New Montane Species of Spiny Pocket Mouse (Rodentia: Heteromyidae: Heteromys) from Northwestern Costa Rica
Fig. 7. Comparisons of female specimens of Heteromys desmarestianus (left column), H. nubicolens (middle column), and H. oresterus (right column); dorsal views of the crania are provided for specimens in age class 5 (top row), age class 4 (middle row), and age class 2 (bottom row). Museum catalog numbers follow: age class 5, KU 158510, KU 142791, and MVZ 164860 (note, zygomatic arches are missing due to breakage); age class 4, KU 158505, KU 159025 (holotype of H. nubicolens), and MVZ 164861; age class 2, MNCR 793, MNCR 797, and MVZ 164862. See appendices 1 and 2 for full provenience.
Fig. 3 in A New Montane Species of Spiny Pocket Mouse (Rodentia: Heteromyidae: Heteromys) from Northwestern Costa Rica
Fig. 3. Dorsal, ventral, and lateral views of the cranium of the holotype of Heteromys nubicolens (KU 159025), an adult female in age class 4. See appendix 1 for full provenience.
Uncovering cryptic pockets in the SARS-CoV-2 spike glycoprotein
<p>The COVID-19 pandemic has prompted a rapid response in vaccine and drug development targeting SARS-CoV-2. Herein, we modelled a complete membrane-embedded SARS-CoV-2 spike (S) protein and used molecular dynamics (MD) simulations in the presence of benzene probes designed to enhance discovery of cryptic, potentially druggable pockets. This approach recapitulated lipid binding sites previously characterized by cryo-electron microscopy, and uncovered a novel cryptic pocket with promising druggable properties located underneath the 617-628 loop, which was shown to be involved in modulating the stability of cleaved S protein trimers a well as the formation of S protein multimers on the viral surface. A multi-conformational behaviour of this loop in simulations was validated using hydrogen-deuterium exchange mass spectrometry (HDX-MS) experiments, supportive of opening and closing dynamics. The pocket is the site of multiple mutations associated with increased transmissibility and severity of infection found in SARS-CoV-2 variants of concern including D614G. Collectively, this work highlights the utility of the benzene mapping approach in uncovering potential druggable sites on the surface of SARS-CoV-2 targets.</p> <p> </p>
Engineering dynamic gates in binding pocket of penicillin G acylase to selectively degrade bacterial signaling molecules
<p>(01-mutants_design.tar.gz) Mutants design:</p> <ol> <li>Input structures of ecPGA from the PDB database (PDB IDs: 1GK9, 1GM7, and 1GM9), processed to resemble wild-type state, repaired by RepairPDB module of FoldX 4</li> <li>Double-point mutants preparation, analysis and filtering: <ol> <li>text files including configuration for FoldX 4</li> <li>inputs and outputs of CAVER 3.02 calculations on FoldX 4 PDB files of ecPGA double-point mutants</li> <li>input configuration file and TransportTools library 0.9.4 calculations outputs generated based on the inputs produced in step 01 and 02 above</li> <li>CSV files containing complete information about FoldX 4 stability prediction and geometrical properties from CAVER 3.02 and TransportTools library version 0.9.4 for ecPGA double-point mutants</li> </ol> </li> <li>Triple-point mutant preparation, analysis and filtering: <ol> <li>text files including configuration for FoldX 4</li> <li>inputs and outputs of CAVER 3.02 calculations on FoldX 4 PDB files of ecPGA triple-point mutants</li> <li>input configuration file and TransportTools library 0.9.4 calculations outputs generated based on the inputs produced in step 01 and 02 above</li> <li>CSV files containing complete information about FoldX 4 stability prediction and geometrical properties from CAVER 3.02 and TransportTools library version 0.9.4 for ecPGA triple-point mutants</li> </ol> </li> </ol> <p>(02-docking.tar.gz) Preparation of protein-ligand complexes using molecular docking for wild-type ecPGA and 6 best designed triple-point mutants with 6 various bacterial signaling molecules:</p> <ol> <li>PDB files of ligand, PDBQT files of the receptor and PDB files of the complexes selected from docking experiment:</li> </ol> <p>Full names of presented protein variants:<br>ecPGA_wt, wild-type Escherichia coli penicillin G acylase<br>LAF, Phe138αLeu & Met142αAla & Ile177βPhe ecPGA variant internally referred as 1GK9_Repair_22<br>LSF, Phe138αLeu & Met142αSer & Ile177βPhe ecPGA variant internally referred as 1GK9_Repair_98<br>MAF, Phe138αMet & Met142αAla & Ile177βPhe ecPGA variant internally referred as 1GK9_Repair_23<br>MSF, Phe138αMet & Met142αSer & Ile177βPhe ecPGA variant internally referred as 1GK9_Repair_99<br>VAF, Phe138αVal & Met142αAla & Ile177βPhe ecPGA variant internally referred as 1GK9_Repair_30<br>YAF, Phe138αTyr & Met142αAla & Ile177βPhe ecPGA variant internally referred as 1GK9_Repair_33<br>Full names of presented AHLs:<br>C06, N-hexanoyl-L-homoserine lactone;<br>C06-3O, N-3-oxo-hexanoyl-L-homoserine lactone;<br>C08, N-octanoyl-L-homoserine lactone;<br>C08-3O, N-3-oxo-octanoyl-L-homoserine lactone;<br>C10, N-decanoyl-L-homoserine lactone;<br>C12-3O, N-3-oxo-dodecanoyl-L-homoserine lactone</p> <p>(03-protein_ligand_MDs.tar.gz) Ligand-enzyme complexes molecular dynamics for wild-type ecPGA and 6 best designed triple-point mutants with 6 various bacterial signaling molecules:</p> <ol> <li>Force field parameters in Amber format</li> <li>Input coordinates *.inpcrd, parameters *.parm7 and *.pdb files for each complex ready for simulation in Amber</li> <li>Amber input files *.in for minimization, equilibration and production runs</li> <li>Restart files for each stage of the minimization, equilibration and production runs in Amber *.rst format</li> <li>Simulation output files for each stage of the minimization, equilibration and production runs in Amber *.mdout format</li> <li>Output files generated during post-processing of production runs trajectories in a form of text files generated by cpptraj</li> </ol> <p>(04-free_enzymes_MDs.tar.gz) Free enzymes molecular dynamics of 3 best triple-point ecPGA (VAF, YAF and MSF) mutants prioritized based on protein-ligand molecular dynamics simulations and experimental assays:</p> <ol> <li>Force field parameters and input coordinates *.inpcrd, parameters *.parm7 and *.pdb files for each complex ready for simulation in Amber format</li> <li>Amber input files *.in for minimization, equilibration and production runs</li> <li>Restart files for each stage of the minimization, equilibration and production runs in Amber *.rst format</li> <li>Simulation output files for each stage of the minimization, equilibration and production runs in Amber *.mdout format</li> <li>Post-processing analysis of generated trajectories: <ol> <li>Text files with distances, CSV files containing result of PCA and clustering, PNG files with clustered PCA results</li> <li>Inputs and outputs of MDpocket analysis and visualization of the pocket frequency grid as an isomesh</li> <li>CAVER input configuration files in text format, CAVER output data including parsed CSV and text files for visualization of entrance opening time evolution and cavity profiles inspection</li> <li>cpptraj generated text files including RMSD, distances and chi1 angles measurements</li> </ol> </li> </ol> <p>All plots were generated using matplotlib or seaborn Python libraries. Figures containing structural representations were generated using PyMOL 2.0.1.</p> <p>(05-ecPGA_VAF_YAF_MSF_penG_MDs.tar.gz) PenG-enzyme complexes molecular dynamics for wild-type ecPGA and 3 best designed triple-point mutants (VAF, YAF, MSF):</p> <ol> <li>PenG force field parameters in Amber (GAFF) format</li> <li>Input coordinates *.inpcrd, parameters *.parm7 and *.pdb files for each complex ready for simulation in Amber</li> <li>Amber input files *.in for minimization, equilibration and production runs</li> <li>Restart files for each stage of the minimization, equilibration and production runs in Amber *.rst format</li> <li>Simulation output files for each stage of the minimization, equilibration and production runs in Amber *.mdout format and analysis output files generated during post-processing of production runs trajectories in a form of text files</li> <li>Reactive Stabilization Score [RSS] statistics summarized in CSV files</li> </ol>
Fluid samples from gingival pockets
<p>Fluid samples from their deepest gingival pocket from a series of hospitalized neurosurgical patients undergoing preoperative dental screening (n=60). The patients were asked whether they brushed their teeth two times a day, once a day and less than every day. For further information or re-use please contact the authors.</p>
Figure 10 in Coleoptera (Histeridae, Leiodidae and Scarabaeidae) inhabiting the burrows of Baird's pocket gopher (Rodentia: Geomyidae: Geomys breviceps) in Arkansas
Figure 10. Collection locations for Cryptoscatomaseter acuminatus. Note: Gray shading represents Geomys spp. distribution. Circles represent published pocket gopher records. Stars represent new Arkansas records.
Figure 2 in Coleoptera (Histeridae, Leiodidae and Scarabaeidae) inhabiting the burrows of Baird's pocket gopher (Rodentia: Geomyidae: Geomys breviceps) in Arkansas
Figure 2. Installation of a burrow pitfall trap: a) burrow is excavated revealing foraging chamber; b) small cup is inserted in bottom of foraging chamber and filled with antifreeze and then a cup containing malt sugar and pig manure is placed above the cup; c) a board is placed over the pitfall and covered with dirt to seal the trap from the surface.
Figure 15 in Coleoptera (Histeridae, Leiodidae and Scarabaeidae) inhabiting the burrows of Baird's pocket gopher (Rodentia: Geomyidae: Geomys breviceps) in Arkansas
Figure 15. Collection locations for Euphoria discicollis. Note: Gray shading represents Geomys spp. distribution. Circles represent published pocket gopher records. Stars represent new Arkansas records.
Figure 9 in Coleoptera (Histeridae, Leiodidae and Scarabaeidae) inhabiting the burrows of Baird's pocket gopher (Rodentia: Geomyidae: Geomys breviceps) in Arkansas
Figure 9. Collection locations for Ptomaphagus geomysi. Note: Gray shading represents Geomys spp. distribution. Circles represent published pocket gopher records. Stars represent new Arkansas records.
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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)
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DANDI Archive for NWB datasets
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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.