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20 results for “Absolute Structure”
Testing absolute plate reference frames and the implications for the generation of geodynamic mantle heterogeneity structure
<div>Description of Resources - Shephard et al. (2012)</div> <div> </div> <div>This file provides a detailed description of all of the files that make up the data collection associated with the publication: Shephard, G. E., Bunge, H. P., Schuberth, B. S., Müller, R. D., Talsma, A. S., Moder, C., & Landgrebe, T. C. W. (2012). Testing absolute plate reference frames and the implications for the generation of geodynamic mantle heterogeneity structure. Earth and Planetary Science Letters, 317, 204-217. doi: <a href="https://doi.org/10.1016/j.epsl.2011.11.027" target="_blank" rel="noopener">10.1016/j.epsl.2011.11.027</a></div> <div> </div> <div>Note: For information on file formats and what programs to use to interact with various file formats, see "File Formats and Recommended Programs”.</div> <div> </div> <div>This data collection includes both the rotations and topologically closed polygons* for each of the 5 absolute reference frames that were tested in the publication. They are to be loaded in GPlates (<a href="http://www.gplates.org" target="_blank" rel="noopener">http://www.gplates.org</a>).</div> <div> </div> <div>*Topologically closed plate polygons are constructed from the intersection of ridges, transforms, subduction zones and other plate boundary geometries. These 'resolved topologies' are valid at 1 Myr intervals. The plate boundary geometries and plate polygons have been assigned plate reconstruction IDs to allow them to be reconstructed using the supplied rotation files. </div> <div> </div> <div>The files associated with this data collection include:</div> <div>• <strong>Hybrid hotspot model (Moving and Fixed hotspots) (HHS)</strong></div> <div>* Caltech_Global_20110311HHS.gpml (37 MB) - topologically closed plate polygons and plate boundary geometries</div> <div>* Caltech_Global_20110412HHS.rot (287 KB)- global rotation model</div> <div> </div> <div>• <strong>Fixed hotspot model (FHS)</strong></div> <div>* Caltech_Global_20110311FHS.gpml (36.8 MB) - topologically closed plate polygons and plate boundary geometries</div> <div>* Caltech_Global_20110412FHS.rot (291 KB) - global rotation model</div> <div> </div> <div>•<strong> Hybrid hotspot and palaeomagnetic model (PMG)</strong></div> <div>* Caltech_Global_20110311PMG.gpml (35.9 MB) - topologically closed plate polygons and plate boundary geometries</div> <div>* Caltech_Global_20110412PMG.rot (287 KB) - global rotation model</div> <div> </div> <div>• <strong>Subduction reference frame model (SUB)</strong></div> <div>* Caltech_Global_20110311SUB.gpml (36 MB) - topologically closed plate polygons and plate boundary geometries</div> <div>* Caltech_Global_20110412SUB.rot (287 KB) - global rotation model</div> <div> </div> <div>• <strong>Hybrid hotspot and TPW-corrected palaeomagnetic model (TPW)</strong></div> <div>* Caltech_Global_20110311TPW.gpml (36.8 MB) - topologically closed plate polygons and plate boundary geometries</div> <div>* Caltech_Global_20110412TPW.rot (287 KB)- global rotation model</div> <div> </div> <div>Project files (.gproj) are included for each .gpml/.rot pair.</div> <div> </div> <div>This article has additional supplementary data available with the online publication.</div> <div> </div> <div> </div> <div>Additional notes:</div> <div>*.rot contains the rotations for all plates and topological polygons.</div> <div>Each model is specific according to the African Plate (Plate ID 701) rotations. The rotations for all other plates are the same across each of the five models with the exception of cross-overs involving Pacific/Panthalassa plates for times earlier than 83.5Ma; these must be absolute reference frame specific and were re-calculated for each model. Programs used to calculate the new finite rotations include "adder" and "seaflow" </div> <div> </div> <div>*.gpml and .shp files contain continuously closing plate polygons i.e. from plate boundaries, from 140 Ma to present-day in 1 million year increments. </div> <div>These files differ slightly from those used in the paper, but are the most up-to-date version (as at May 2011) and are based on an updated model, Seton et al. (2012).</div> <div>They are specific to each of the five absolute reference frames. </div> <div> </div> <div>Note on velocity calculations in GPlates:</div> <div>GPlates calculates the velocity within each plate based on the stage rotation for that time period and averages for that respective period. For this reason, the velocities of a plate do not change incrementally within the time period and then abruptly change according to the next time period/stage rotation. </div> <div>This is also why there appears to be a "jump" in velocity magnitude and direction between 140 and 139 Ma.</div>
Pose Selector Workflow - Docking Poses, Absolute Binding Free Energy Estimates and Structure Input Files for Machine Learning
<p>The Pose Selector (PS) workflow calculates absolute binding free energies (ABFEs) for binding poses of protein-ligand complexes. First, it converts the binding poses (both docking poses as well as experimentally observed ligand binding poses), which are provided as a combination of protein PDB file and ligand MOL2 file, into input files for molecular dynamics (MD) simulations with GROMACS after they have passed extensive quality checks and repair steps. Next, the PS workflow post-processes and analyses the last frame of the resulting eight 100 ps trajectories per binding pose with the Generalised Born model of implicit solvation as implemented in gmx_MMPBSA to obtain the ABFE estimates. The workflow was designed for soluble proteins without post-translational modifications, co-factors and non-standard amino acids, and it has limited support for coordinated ions.</p> <p>For the dataset published here, the PS workflow was run on docking poses generated for the PDBbind 2020 dataset (http://www.pdbbind.org.cn/index.php), shared in dockingPosesPDBBind2020.tar.gz. This entry and its partner entry 10.5281/zenodo.11397486 also share the intial coordinates used in the MD simulations of >800,000 docking poses of 4022 protein-ligand complexes (structureFiles_dockingPoses1.tar.gz in this entry and structureFiles_dockingPoses2.tar.gz in 10.5281/zenodo.11397486) and of the experimental ligand binding pose of 4549 complexes (structureFiles_experimentalStructures.tar.gz) as well as the corresponding ABFE estimates (absoluteBindingFreeEnergyEstimates.tar.gz). The MD simulations were run on the LUMI and MeluXina supercomputers while the implicit-solvent calculations were carried out on Galileo (Cineca).</p> <p>The README file describes the structure of the shared data in more detail and points out how to reproduce the MD trajectories and the subsequent implicit-solvent calculations yielding the free-energy estimates as well as how to use the data provided in this entry to train a machine-learning model predicting the ABFE of binding poses of protein-ligand complexes. The workflow scripts can be downloaded from GitHub (https://github.com/LigateProject/Pose-Selector-workflow). The MD simulations were run with GROMACS 2023.2 (https://manual.gromacs.org/2023.2/index.html), and the implicit-solvent calculations were carried out with gmx_MMPBSA 1.6.1 (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/v1.6.1/).</p>
Fig. 8 in Structures and absolute configurations of butenolide derivatives from the isopod-associated fungus Pidoplitchkoviella terricola
Fig. 8. (A) The binding mode of 10 (yellow) in complex with mushroom tyrosinase. Hydrogen bonds interactions were indicated by dotted red lines. (B) Compound 10 was docked into the binding pocket of the mushroom tyrosinase. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 6 in Structure elucidation and absolute configuration determination of C , C and C tirucallane triterpenoids from the leaves of Picrasma quassioides (D. Don) Benn
Fig. 6. (A) The ORTEP diagram of 8a (Cu Kα). (B) Synthesis of 8a: EDCI, DMAP, CH2Cl2, r. t., 48h, 70.6%.
Fig. 4 in Structure elucidation and absolute configuration determination of C , C and C tirucallane triterpenoids from the leaves of Picrasma quassioides (D. Don) Benn
Fig. 4. Comparison of the experimental and calculated ECD spectra of 1–7 in MeOH. Spectra were calculated at the B3LYP/6–311++ G(2d,p)//B3LYP/6-31G (d) level.
Fig. 8 in Structure elucidation and absolute configuration determination of C , C and C tirucallane triterpenoids from the leaves of Picrasma quassioides (D. Don) Benn
Fig. 8. Cytotoxic activities of compounds 1–16 against two hepatocellular carcinoma cell lines. (A) Inhibition ratio of all isolates at 50.0 μM. Sora: sorafenib at 16.0 μM, positive control. (B) Compounds with inhibition ratios> 40% were screened out to treat HepG2 cells in subsequent experiments and cell viability was determined by MTT assays.
Fig. 7 in Structure elucidation and absolute configuration determination of C , C and C tirucallane triterpenoids from the leaves of Picrasma quassioides (D. Don) Benn
Fig. 7. Influence of different configurations of 23-OCH on the δ (C-23, C24, C25) and δ (H-23, H-24) values of compounds 7–10 (1 H NMR 600 MHz, 13C NMR 3 C H 150 MHz).
Fig. 2. A in Structure elucidation and absolute configuration of metabolites from the soil-derived fungus Dictyosporium digitatum using spectroscopic and computational methods
Fig. 2. A: Key HMBC and COSY correlations of 1. B: Key NOESY correlations of 1. C: Mosher's ester analysis of MTPA-1 (irregular ΔδS−R signs in bold). D: Key HMBC and COSY correlations for dictyosporin C (3). E: Key NOESY correlations of 3. F: Octant rules applied for 3. G: Key HMBC and COSY correlations of dictyosporin D (4). H: Key NOESY correlations of 4. I: Experimental ECD spectrum of 4 and calculated ECD spectra of (1S, 10S)-4 and (1R, 10R)-4.
Fig. 4 in Structures and absolute configurations of butenolide derivatives from the isopod-associated fungus Pidoplitchkoviella terricola
Fig. 4. Comparison of the calculated vs experimental ECD spectra in MeOH for compound 5.
Fig. 3 in Structures and absolute configurations of butenolide derivatives from the isopod-associated fungus Pidoplitchkoviella terricola
Fig. 3. Δδ values (in ppm) = δS - δR obtained for (S)- and (R)- MPTA esters (1a–5a and 1b–5b).
Fig. 2 in Structures and absolute configurations of butenolide derivatives from the isopod-associated fungus Pidoplitchkoviella terricola
Fig. 2. Key COSY and HMBC correlations of compounds 1–7.
Fig. 1 in Structures and absolute configurations of butenolide derivatives from the isopod-associated fungus Pidoplitchkoviella terricola
Fig. 1. The structures of compounds 1–20.
Fig. 6 in Structures and absolute configurations of butenolide derivatives from the isopod-associated fungus Pidoplitchkoviella terricola
Fig. 6. Comparison of the calculated and experimental ECD spectra in MeOH for compound 6.
Fig. 3 in Structure elucidation and absolute configuration determination of C , C and C tirucallane triterpenoids from the leaves of Picrasma quassioides (D. Don) Benn
Fig. 3. Key NOESY correlations of compounds 1–7.
Fig. 2. Key 1H–1H in Structure elucidation and absolute configuration determination of C , C and C tirucallane triterpenoids from the leaves of Picrasma quassioides (D. Don) Benn
Fig. 2. Key 1H–1H COSY and HMBC correlations of compounds 1–7.
Fig. 5 in Structure elucidation and absolute configuration determination of C , C and C tirucallane triterpenoids from the leaves of Picrasma quassioides (D. Don) Benn
Fig. 5. The ORTEP drawings of compounds 1 and 7 (Cu Kα).
Fig. 1 in Structure elucidation and absolute configuration determination of C , C and C tirucallane triterpenoids from the leaves of Picrasma quassioides (D. Don) Benn
Fig. 1. The structures of compounds 1–16.
Fig. 1 in Structure elucidation and absolute configuration of metabolites from the soil-derived fungus Dictyosporium digitatum using spectroscopic and computational methods
Fig. 1. Structures of compounds 1–16.
Fig. 5 in Structures and absolute configurations of butenolide derivatives from the isopod-associated fungus Pidoplitchkoviella terricola
Fig. 5. Preparation of acetomide derivative 6a.
Fig. 7 in Structures and absolute configurations of butenolide derivatives from the isopod-associated fungus Pidoplitchkoviella terricola
Fig. 7. Experimental ECD spectra in MeOH for 1 and 7.
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