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598 results for “Small molecules”
Vibrational Neutron Spectroscopy Data for Small Molecule Organic Semiconductors
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Data from: Small molecule protein assembly modulators with Pan-Cancer therapeutic efficacy
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Simulation input and out and data analysis for calculating partition coefficients of small molecules in octanol/water and cyclohexane/water
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Small molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer's disease
<p>These data describe the bound and unbound ensembles of a disordered peptide (amyloid beta) in the presence and absence of a small, drug-like molecule. The data were produced by metadynamic metainference simulations restrained with NMR chemical shift data. We used PLUMED version 2.6.0 and GROMACS 2018.3. All the data and PLUMED input files required to reproduce the metadynamic metainference results are available on PLUMED-NEST (www.plumed-nest.org), the public repository of the PLUMED consortium, as plumID:20.014.</p> <p>A Jupyter Notebook describing the analysis of these results is available from GitHub at https://github.com/vendruscolo-lab/amyloid-beta_small_mol/ in Metadynamic_metainference/Analysis.</p> <p>These data support the findings of the manuscript entitled "Small molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer's disease" by Heller <em>et al</em>. DOI: 10.1101/729392</p>
Discovery of Novel small-molecule dual inhibitor targeting toll-like receptors 7 and 9
<p>The data sets contained the MD simulation of TLR7-TIC10g and TLR9-TIC10g complexes.</p>
Phase field simulations of thermal annealing for all-small molecule organic solar cells
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Dataset: Modeling of small molecule's affinity to phospholipids using IAM-HPLC and QSRR approach enhanced by similarity-based machine algorithms
<div>Dataset for publication</div>
Dataset: Modification of Gradient HPLC Method for Determination of Small Molecules' Affinity to Human Serum Albumin under Column Safety Conditions: Robustness and Chemometrics Study
<p>Dataset for publication.</p> <p> </p>
Radiation Damage in Small Molecule Crystallography - Experiment 7
<p>Seventh data set in a series of experiments investigating the effect of radiation damage to a small molecule crystal structure.</p> <p>Sample: catena-(bis(m2-Glycyl-histidinato-N,N',O)-nickel(II) heptahydrate)</p> <p>sum formula: C16H36N8NiO13</p> <p>Wavelength: 0.9889 Angstrom</p> <p>Temperature: 60 K</p> <p>Flux: 2.63•10<sup>10 </sup>ph/s</p> <p>Calculated dose (DWD) per scan: 1.92MGy</p>
Dataset from publication Modeling of small molecule's affinity to phospholipids using IAM-HPLC andQSRR approach enhanced by similarity-based machine algorithms
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VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations
<p>The tar file contains all the files related to the two case studies presented in the article. </p>
Synthesis and preclinical evaluation of a novel fluorine-18 labeled small-molecule PET radiotracer for imaging of CXCR3 receptor in mouse models of atherosclerosis
<p>Background CXCR3 is a chemokine receptor and is expressed in innate and adaptive immune cells. It promotes<br> the recruitment of T-lymphocytes and other immune cells to the inflammatory site in response to the binding of cognate<br> chemokines. Upregulation of CXCR3 and its chemokines has been found during atherosclerotic lesion formation.<br> Therefore, detection of CXCR3 by positron emission tomography (PET) radiotracer can be a useful tool for detecting the development of atherosclerosis in a noninvasive manner. Herein, we report the synthesis, radiosynthesis, and characterization of a novel fluorine-18 (F-18, <sup>18</sup>F) labeled small-molecule radiotracer for the imaging of the CXCR3 receptor in mouse models of atherosclerosis.<br> Results The reference standard <strong>1</strong> and its precursor <strong>9</strong> were synthesized over 5 steps from starting materials in good to moderate yields. The measured K<sub>i</sub> values of CXCR3A and CXCR3B were 0.81 ± 0.02 nM and 0.31 ± 0.02 nM, respectively. [<sup>18</sup>F]<strong>1</strong> was prepared by a two-step radiosynthesis with a decay-corrected radiochemical yield of 13 ± 2%, radiochemical purity > 99%, and specific activity of 44.4 ± 3.7 GBq/μmol at the end of synthesis (n = 6). The baseline studies showed that [<sup>18</sup>F]<strong>1</strong> displayed high uptake in the atherosclerotic aorta and brown adipose tissue in Apolipoprotein E (ApoE) knockout (KO) mice fed with a high-fat diet over 12 weeks. The uptake of [<sup>18</sup>F]<strong>1</strong> in these regions was reduced significantly in self-blocking studies, demonstrating CXCR3 binding specificity. Contrary to this, no significant differences in uptake of [<sup>18</sup>F]<strong>1</strong> in the abdominal aorta of C57BL/6 control mice fed with a normal diet were observed in both baseline and blocking studies, indicating increased CXCR3 expression in atherosclerotic lesions. Immunohistochemistry studies demonstrated that [<sup>18</sup>F]<strong>1</strong>-positive regions were correlated with CXCR3 expression, but some<br> atherosclerotic plaques with significant size were not detected by [<sup>18</sup>F]<strong>1</strong>, and their CXCR3 expressions were minimal.<br> Conclusion [<sup>18</sup>F]<strong>1</strong> was synthesized with good radiochemical yield and high radiochemical purity. In PET imaging<br> studies, [<sup>18</sup>F]<strong>1</strong> displayed CXCR3-specific uptake in the atherosclerotic aorta in ApoE KO mice. [<sup>18</sup>F]<strong>1</strong> visualized CXCR3<br> expression in different regions in mice aligned with the tissue histology studies. Taken together, [<sup>18</sup>F]<strong>1</strong> is a potential<br> PET radiotracer for imaging CXCR3 in atherosclerosis.</p>
Fig. 7 in HSQC-based small molecule accurate recognition technology discovery of diverse cytotoxic sesquiterpenoids from Elephantopus tomentosus L. and structural revision of molephantins A and B
Fig. 7. The ORTEP drawing of 9–11.
Fig. 6 in HSQC-based small molecule accurate recognition technology discovery of diverse cytotoxic sesquiterpenoids from Elephantopus tomentosus L. and structural revision of molephantins A and B
Fig. 6. Experimental and calculated ECD spectra of 2, 3, 5, 8, and 12.
Fig. 4 in HSQC-based small molecule accurate recognition technology discovery of diverse cytotoxic sesquiterpenoids from Elephantopus tomentosus L. and structural revision of molephantins A and B
Fig. 4. Key NOESY correlations of 1–12.
Fig. 3. Key HMBC and 1 H– 1 H in HSQC-based small molecule accurate recognition technology discovery of diverse cytotoxic sesquiterpenoids from Elephantopus tomentosus L. and structural revision of molephantins A and B
Fig. 3. Key HMBC and 1 H– 1 H COSY correlations of 1–12.
Fig. 2. Compounds 1–15 isolated from E. tomentosus L in HSQC-based small molecule accurate recognition technology discovery of diverse cytotoxic sesquiterpenoids from Elephantopus tomentosus L. and structural revision of molephantins A and B
Fig. 2. Compounds 1–15 isolated from E. tomentosus L.
Fig. 6 in Recent advances in inducing endophytic fungal specialized metabolites using small molecule elicitors including epigenetic modifiers
Fig. 6. Some metabolites induced through organic solvent elicitation.
Inhibition of the α4β1 integrin activity by small Tellurium molecules Regulates PD-L1 Expression and Enhances Anti-Tumor Effect
<p>Figs source data</p>
Augmented base pairing networks encode RNA-small molecule binding preferences
<p>Dataset used to train and validate the RNAmigos model from "Augmented base pairing networks encode RNA-small molecule binding preferences".</p> <p> </p> <p>This will give you a cleaned up version of the data used to train the RNAmigos 1.0 models.</p> <p> </p> <p>If you run `python make_nice.py` you will generate a CSV file `rnamigos1_dataset.csv` which contains all the info you need.</p> <p>The script will also use DecoyFinder to generate the decoys for each pocket.</p> <p> </p> <p> </p> <p>### Pockets</p> <p> </p> <p>The CSV has one row for each binding pocket.</p> <p> </p> <p>The columns are:</p> <p> </p> <p>* pdbid: the PDBID this pocket belongs to</p> <p>* model_num: the model number inside the PDB we took</p> <p>* chain: the chain the pocket belongs to</p> <p>* ligand_id: the 3-letter code of the ligand (e.g. ATP) which you can look up on RCSB.org</p> <p>* ligand_resnum: the residue number of the ligand in the PDB</p> <p>* nodelist: a list of nodes separated by ';' in the pocket as a string in the format `<node1 pdbid>.<node1 chain>.<node1 position>-<nucleotide type>;<node2 pdbid>...`</p> <p>* edgelist: a list of edges separated by ';' in the pocket as a string in the format nodes are in the same format as above, and connected by a '-' char, with an additional label field. e.g. of a two edge list `1aju.A.1-1aju.A.5-CWW;1aju.A.1-1aju.A.2-B53`</p> <p>* fp_native_maccs: bit string of the MACCS for the native ligand</p> <p>* split_{k}_train: one col for all the splits we ran (k \in {0-9}) contains True if this pocket was in the train set for this split</p> <p>* split_{k}_test: one col for all the splits we ran (k \in {0-9}) contains True if this pocket was in the test set for this split</p> <p> </p> <p>### Decoys</p> <p> </p> <p>The folder `decoy_db/` has the following structure:</p> <p> </p> <p>```</p> <p>decoy_db</p> <p> <pdbid>_<chain>_{ligand_id}_{ligand_position}</p> <p> decoyfinder</p> <p> actives.txt</p> <p> decoys.txt</p> <p> pdb</p> <p> actives.txt</p> <p> decoys.txt</p> <p> </p> <p> </p> <p>Each `actives.txt` and `decoys.txt` is a file with one SMILES per line. </p> <p> </p> <p>`decoyfinder/` has decoys computed by DecoyFinder and the acvtives are just the native ligands.</p> <p>`pdb/` has decoys taken from other pockets in the PDB and actives are just the native ligands.</p>
ScienceDex guides
Understand access before you commit
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.