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13 results for “Surface ligands”
Code for manuscript "Organic ligands in whale excrement support iron availability and reduce copper toxicity to the surface ocean" by Monreal et al.
<p>.zip file containing GitHub repository titled "ligands-in-whale-excrement" (<a href="https://github.com/patrickmon38/ligands-in-whale-excrement/tree/main">https://github.com/patrickmon38/ligands-in-whale-excrement/tree/main</a>)<br><br><strong>README from GitHub: </strong></p> <div> <h3>Code used to generate figures for the manuscript "Organic ligands in whale excrement support iron availability and reduce copper toxicity to the surface ocean" by Monreal et al. are found in this repository.</h3> </div> <div> <p>In press at Communications Earth & Environment</p> <p> </p> </div> <p>Most data (all except .mzXML data) called in code is from Github_Data_For_Whale_Ligand_Manuscript.xlsx in this repository.</p> <p> </p> <p>Mass spec data from .mzXML files are has been depositied and is available for download in the Mass Spectrometry Interactive Virtual Environment (MassIVE). LC-ESI-MS (Orbitrap) and LC-FT-ICR-MS raw data can be accessed there under MSV000094994 (doi:10.25345/C50000B5D) and MSV000094995 (doi:10.25345/C5V98034P), respectively.</p> <p> </p> <p>html output from Rmarkdown file can be viewed directly at <a href="https://html-preview.github.io/?url=https://github.com/patrickmon38/ligands-in-whale-excrement/blob/main/Figures_for_GitHub_Whale_Excrement_Manuscript.html" rel="nofollow">https://html-preview.github.io/?url=https://github.com/patrickmon38/ligands-in-whale-excrement/blob/main/Figures_for_GitHub_Whale_Excrement_Manuscript.html</a>.</p> <p>If trying to run Rmarkdown on your own system, you will need to download the .xlsx and .mzXML files and change paths accordingly.</p> <p>Co-authors of this manuscript:</p> <h5>Patrick J. Monreal (University of Washington)</h5> <h5>Matthew S. Savoca (Stanford University)</h5> <h5>Lydia Babcock-Adams (National High Magnetic Field Laboratory)</h5> <h5>Laura E. Moore (University of Washington)</h5> <h5>Angel Ruacho (Univesrity of Washington)</h5> <h5>Dylan Hull (University of Washington)</h5> <h5>Logan J. Pallin (Unversity of California, Santa Cruz)</h5> <h5>Ross C. Nichols (Unversity of California, Santa Cruz)</h5> <h5>John Calambokidis (Cascadia Research Collective)</h5> <h5>Joseph A. Resing (Unviersity of Washington/CICOES/NOAA)</h5> <h5>Ari S. Friedlaender (Unversity of California, Santa Cruz)</h5> <h5>Jeremy Goldbogen (Stanford University)</h5> <h5>Randelle M. Bundy (University of Washington)</h5> <p> </p> <div> </div> <div><strong>If there are issues or questions with the code, author for contact is Patrick Monreal (<a href="mailto:pmonreal@uw.edu">pmonreal@uw.edu</a>).</strong></div>
Data used in article 'Tuning Charge Carrier Dynamics and Surface Passivation in Organolead Halide Perovskites with Capping Ligands and Metal Oxide Interfaces'
<p>Data underlying the article 'Tuning Charge Carrier Dynamics and Surface Passivation in Organolead Halide Perovskites with Capping Ligands and Metal Oxide Interfaces' published in Advanced Optical Materials.</p>
Speciation and Structures in Pt Surface Sites Stabilized by N-Heterocyclic Carbene Ligands Revealed by DNP Enhanced Indirect-ly Detected 195Pt NMR Spectroscopic Signatures and Fingerprint Analysis
<p>Raw NMR data for the paper published under DOI: 10.1021/jacs.2c08300</p>
Data for "Binding Affinity of Monoalkyl Phosphinic Acid Ligands toward Nanocrystal Surfaces".
<p>Data of the figures in the publication "<strong>Binding Affinity of Monoalkyl Phosphinic Acid Ligands toward Nanocrystal Surfaces</strong>".</p> <p>The <em>.pxp</em> documents contain the experimental data of the figures in the manuscript and they can be opened/edited with the software IGOR Pro 6.3 or higher.</p> <p>Table of contents:</p> <p><strong>Figure 1.</strong> (A) General reaction scheme toward monoclinic HfO<sub>2</sub>/oleate NCs. (B) TEM image and (C) DOSY NMR spectrum in C<sub>6</sub>D<sub>6</sub> of HfO<sub>2</sub>/oleate NCs. (D) General reaction scheme toward zinc blend CdSe/oleate NCs. (E) TEM image and (F) DOSY NMR spectrum in C<sub>6</sub>D<sub>6</sub> of CdSe/oleate NCs.</p> <p><strong>Figure 2.</strong> (Left) Titration of HfO<sub>2</sub>/oleate with 6-(hexyloxy)hexylphosphinic acid. (A) General reaction scheme. (B) <sup>1</sup>H NMR spectra of the titration. (C) <sup>31</sup>P NMR after 0.95 and 1.15 equiv of phosphinic acid is added. (D) Quantification of the different compounds as a function of the added equivalents. (Right) Titration of CdSe/oleate with 6-(hexyloxy)hexylphosphinic acid. (E) General reaction scheme. (F) <sup>1</sup>H NMR spectra of the titration. (G) <sup>31</sup>P NMR after 1.0 and 1.2 equiv of phosphinic acid is added. (H) Quantification of the different compounds as a function of the added equivalents.</p> <p><strong>Figure 3.</strong> (A) <sup>1</sup>H NMR spectrum of oleate-capped HfO<sub>2</sub> NCs in C<sub>6</sub>D<sub>6</sub>. (B) <sup>1</sup>H NMR spectrum of HfO<sub>2</sub> in C<sub>6</sub>D<sub>6</sub> after ligand exchange for 6-(hexyloxy)hexylphosphinic acid and purification. The inset shows the <sup>31</sup>P NMR spectrum.</p> <p><strong>Figure 4.</strong> (Left) Titration of HfO<sub>2</sub>/[6-(hexyloxy)hexyl]phosphinate with oleylphosphonic acid. (A) General reaction scheme. (B) <sup>1</sup>H NMR spectra of the titration. (C) Quantification of the different compounds as a function of the added equivalents. Note that the small amount of residual oleic acid present at the start of the titration in (B) is due to a challenging purification (high solubility of the HfO<sub>2</sub>/[6-(hexyloxy)hexyl]phosphinate NCs). This small signal was integrated and subtracted from the spectra for the quantification in (C). (Right) Titration of CdSe/[6-(hexyloxy)hexyl]phosphinate with oleylphosphonic acid. (D) General reaction scheme. (E) <sup>1</sup>H NMR spectra of the titration. (F) Quantification of the different compounds as a function of the added equivalents.</p> <p><strong>Figure 5.</strong> Mole fraction of bound oleylphosphonate in the ligand shell, χ<sub>phosphon (bound)</sub>, as a function of the overall mole fraction of oleylphosphonic acid (=unbound phosphonic acid and bound phosphonate), χ<sub>phosphon (total)</sub>, during the titrations of HfO<sub>2</sub> (blue), CdSe (red), and ZnS (green) NCs. The full lines represent different calculated equilibrium constants.</p> <p><strong>Figure 6.</strong> Mole fraction of a bound incoming ligand (= titrating ligand) in the ligand shell, χ<sub>incomingligand (bound)</sub>, as a function of the overall mole fraction of the total incoming ligand (=unbound and bound), χ<sub>incomingligand (total)</sub>, during the titrations of ZnS NCs stabilized with a 50/50 mixture of <em>n</em>-hexyl/<em>n</em>-octadecylphosphinate with oleylphosphonic acid (gray), ZnS NCs stabilized with 6-(hexyloxy)hexylphosphinate with oleylphosphonic acid (green) and ZnS NCs stabilized with oleate with a 50/50 mixture of <em>n</em>-hexyl/<em>n</em>-octadecylcarboxylic acids (orange). The full lines represent the different calculated equilibrium constants.</p> <p><strong>Figure S1.</strong> (A) HfO2/oleate NCs, (B) 1H NMR spectrum in C6D6, and (C) DOSY decay curve of the alkene region.</p> <p><strong>Figure S2.</strong> (A) CdSe/oleate NCs, (B) 1H NMR spectrum in C6D6, and (C) UV-vis absorption spectrum, (D) DOSY decay curve of the alkene region, and (E) DOSY decay curve of the methylene region.</p> <p><strong>Figure S3.</strong> Synthesis of zinc blende ZnS/oleate NCs. (A) General reaction scheme, (B) TEM image, and (C) 1H NMR spectrum in C6D6, (D) DOSY NMR spectrum in C6D6, (E) DOSY decay curve of the alkene region, and (F) UV-vis absorption spectrum.</p> <p><strong>Figure S4.</strong> 1H NMR of (top, black line) the supernatant of the HfO2/oleate NCs after titration until 1.0 equivalent 6-(hexyloxy)hexyl phosphinic acid is added, and (bottom grey line) reference spectrum of oleic acid in CDCl3.</p> <p><strong>Figure S5.</strong> 1H NMR of (top, black line) the supernatant of the CdSe/oleate NCs after titration until 1.0 equivalent 6-(hexyloxy)hexyl phosphinic acid is added, and (bottom grey line) reference spectrum of oleic acid in CDCl3</p> <p><strong>Figure S6.</strong> Titration of ZnS/oleate NCs with 6-(hexyloxy)hexylphosphinic acid. (A) General reaction scheme, (B) 1H NMR spectra of the titration, (C) 31P NMR after 1.0 and 1.6 equivalent phosphinic acid is added, and (D) quantification of the different compounds as a function of added equivalents.</p> <p><strong>Figure S7.</strong> 1H and 31P NMR spectra of (top gray line) n-tetradecylphosphinic acid dehydrated<br>with dicyclohexylcarbodiimide (DCC) to form n-tetradecylphosphinic anhydride, and (bottom<br>black line) n-tetradecylphosphinic acid reference, both in C6D6. </p> <p><strong>Figure S8.</strong> (A) 1H and (B) 31P NMR of (top black line) the supernatant of the ZnS/oleate NCs after titration until 1.6 equivalent 6-(hexyloxy)hexylphosphinic acid is added, and reference spectra of (red line) oleic acid and (blue line) 6-(hexyloxy)hexylphosphinic acid in CDCl3.</p> <p><strong>Figure S9.</strong> Purified HfO2/[6-(hexyloxy)hexyl]phosphinate NCs. (A) HfO2/phosphinate NCs. (B) 1H NMR spectrum in C6D6 with zoom inset of the broadened P-H resonance, (C) 31P NMR spectrum in C6D6, (D) DOSY NMR spectrum in C6D6, (E) DOSY decay curve of the ether region.</p> <p><strong>Figure S10.</strong> Purified CdSe/[6-(hexyloxy)hexyl]phosphinate NCs. (A) CdSe/phosphinate NCs. (B) 1H NMR spectrum in C6D6, (C) 31P NMR spectrum in C6D6, (D) DOSY NMR spectrum in C6D6, (E) DOSY decay curve of the ether region, (F) DOSY decay curve of the methylene region, and (G) UV-vis absorption spectrum.</p> <p><strong>Figure S11.</strong> Purified ZnS/[6-(hexyloxy)hexyl]phosphinate NCs. (A) ZnS/phosphinate NCs. (B) 1H NMR spectrum in C6D6 with zoom inset of the broadened P-H resonance, (C) 31P NMR spectrum in C6D6, (D) DOSY NMR spectrum in C6D6, (E) DOSY decay curve of the ether region, and (F) UV-vis absorption spectrum.</p> <p><strong>Figure S12.</strong> (A) 1H and (B) 31P NMR of the supernatant (black line) of the HfO2/phosphinate NCs after titration until 2.0 equivalent oleylphosphonic acid is added, and reference spectra of (green line) oleylphosphonic acid and (blue line) 6-(hexyloxy)hexylphosphinic acid in C6D6</p> <p><strong>Figure S13.</strong> (A) 1H and (B) 31P NMR of the supernatant (black line) of the CdSe/phosphinate NCs after titration until 2.0 equivalent oleylphosphonic acid is added, and reference spectra of (green line) oleylphosphonic acid and (blue line) 6-(hexyloxy)hexylphosphinic acid in C6D6. </p> <p><strong>Figure S14.</strong> Titration of ZnS/[(6-hexyloxy)hexyl]phosphinate with oleylphosphonic acid. (A) General reaction scheme, (B) 1H NMR spectra of the titration, and (C) quantification of the different compounds as a function of added equivalents.</p> <p><strong>Figure S15.</strong> (A) 1H and (B) 31P NMR of the supernatant (black line) of the ZnS/phosphinate NCs after titration until 2.0 equivalent oleylphosphonic acid is added, and reference spectra of (green line) oleylphosphonic acid and (blue line) 6-(hexyloxy)hexyl phosphinic acid in C6D6.</p> <p><strong>Figure S16.</strong> Titration of HfO2 NCs stabilized with a mixed ligand shell consistent of 6-(hexyloxy)hexylphosphinate and oleylphosphonate. (A) General reaction scheme, (B) 1H NMR spectrum of the purified NCs prior to titration (at 0.0 added equivalents of 6-(hexyloxy)hexylphosphinic acid), (C) 1H NMR spectra of the titration, and (D) quantification of the different compounds as a function of added equivalents 6-(hexyloxy)hexylphosphinic acid.</p> <p><strong>Figure S17.</strong> Titration of CdSe NCs stabilized with a mixed ligand shell consistent of 6-(hexyloxy)hexylphosphinate and oleylphosphonate. (A) General reaction scheme, (B) 1H NMR spectrum of the purified NCs prior to titration (at 0.0 added equivalents of 6-(hexyloxy)hexylphosphinic acid), (C) 1H NMR spectra of the titration, and (D) quantification of the different compounds as a function of added equivalents 6-(hexyloxy)hexylphosphinic acid.</p> <p><strong>Figure S18.</strong> Titration of ZnS NCs stabilized with a mixed ligand shell consistent of 6-(hexyloxy)hexylphosphinate acid and oleylphosphonate. (A) General reaction scheme, (B) 1H NMR spectrum of the purified NCs prior to titration (at 0.0 added equivalents of 6-(hexyloxy)hexylphosphinic acid) (C) 1H NMR spectra of the titration, and (D) quantification of the different compounds as a function of added equivalents 6-(hexyloxy)hexylphosphinic acid.</p> <p><strong>Figure S19.</strong> The mole fraction of bound oleylphosphonate in the ligand shell, 𝜒𝑝ℎ𝑜𝑠𝑝ℎ𝐨𝑛 (𝑏𝑜𝑢𝑛𝑑), as a function of the overall mole fraction of oleylphosphonic acid (= unbound phosphonic acid and bound phosphonate), 𝜒𝑝ℎ𝑜𝑠𝑝ℎ𝐨𝑛 (𝑡𝑜𝑡𝑎𝑙) , during the titrations of (A) HfO2 (blue), (B) CdSe (red), and (C) ZnS (green) NCs. The full lines represent different calculated equilibrium constants.</p> <p><strong>Figure S20.</strong> Changes in chemical shift during the ligand exchange of phosphinate for phosphonate for HfO2, CdSe, and ZnS NCs</p> <p><strong>Figure S21.</strong> Purified ZnS/n-alkylphosphinate NCs with a 50/50 mixture of n-hexyl/noctadecylphosphinate. (A) ZnS/phosphinate NCs. (B) 1H NMR spectrum in C6D6 with zoom inset of the broadened P-H resonance, (C) 31P NMR spectrum in C6D6, (D) DOSY NMR spectrum in C6D6, (E) DOSY decay curve of the alkane region, and (F) UV-vis absorption spectrum.</p> <p><strong>Figure S22.</strong> Titration of ZnS/n-alkylphosphinate with a 50/50 mixture of n-hexyl/noctadecylphosphinate with oleylphosphonic acid. (A) General reaction scheme, (B) 1H NMR spectra of the titration (zoom of the alkene resonance and the adjacent methylene groups), and (C) quantification of the different compounds as a function of added equivalents.</p> <p><strong>Figure S23.</strong> Comparative ligand exchange experiments where oleate capped ZnS NCs are titrated with a 50/50 mixture of n-hexyl/n-octadecylcarboxylic, -phosphinic, or -phosphonic acids. (A) General reaction scheme for the 3 separate titrations with carboxylic, phosphinic, or phosphonic acids. (B) Bound fraction of oleate on ZnS NCs as a function of the added equivalents of the titrating acid mixture, including the theoretical expected quantitative and random exchange development.</p> <p><strong>Figure S24.</strong> Titration of ZnS/oleate NCs with a 50/50 mixture of n-hexyl, and n-octadecyl carboxylic, phosphinic, and phosphonic acids in C6D6. (A) General reaction scheme. (B) 1H NMR spectra of the titration with carboxylic acids. (C) 1H NMR spectra of the titration with phosphinic acids. (D) 1H NMR spectra of the titration with phosphonic acids (added from a concentrated solution in THF-d8).</p> <p> </p> <p> </p> <p> </p>
Research data supporting "Surface dynamics and ligand-core interactions of quantum size photoluminescent gold nanoclusters"
<p>Experimental research raw data supporting the publication by Lin, Y. et al, 2018, Surface dynamics and ligand-core interactions of quantum sized photoluminescent gold nanoclusters, Journal of the American Chemical Society. DOI: 10.1021/jacs.8b04436</p> <p>Molecular simulation data is available upon reasonable request from irene.yarovsky@rmit.edu.au.</p>
Mapping out the aqueous surface chemistry of metal oxide nanocrystals; carboxylate, phosphonate and catecholate ligands
<p>Data underlying the figures in the publication “Mapping out the aqueous surface chemistry of metal oxide nanocrystals; carboxylate, phosphonate and catecholate ligands”, published in JACS Au.</p> <p> </p> <p>Table of contents:</p> <p>The <em>.pxp</em> documents contain the experimental data of the figures in the manuscript and it can be opened/edited with the software IGOR Pro 8.0 or higher.</p> <p><strong>1. Figure 1.pxp</strong>: Experimental data for <em>Figure 1</em>. (A) Solvothermal synthesis of HfO<sub>2</sub> nanocrystals starting from 1 equivalent Hf(O-tBu)<sub>4</sub> and 80 equivalents benzyl alcohol. (B) <sup>1</sup>H NMR spectra (normal or diffusion filtered) of MEEAA functionalized HfO<sub>2</sub> NCs in different solvents. The α and β resonances belong to the residual hydroxyl and methyl groups of methanol, respectively. (C) Transmission Electron Microscopy (TEM) image of the synthesized HfO<sub>2</sub> NCs. The NC diameter of the quasi-spherical NCs was calculated after measuring the surface area of at least 150 NCs and calculated the diameter as if it was a circle. A size distribution histogram and a zoomed-in image of a singular NC can be seen respectively in the bottom left and the top right corner.</p> <p><strong>2. Figure 2.pxp</strong>: Experimental data for <em>Figure 2</em>. (A) Ligand exchange performed between MEEAA functionalized NCs and PA-PEG. (B) <sup>1</sup>H NMR reference spectra in MeOD of the free ligands as reference and the stepwise titration of MEEAA functionalized NCs with PA-PEG, equivalents are with respect to the total amount of MEEAA present. (C) <sup>31</sup>P NMR spectra (4096 scans) in MeOD for the stepwise titration of MEEAA functionalized NCs with PA-PEG, broadened signals are indicative of NC binding. (D) Diffusion filtered <sup>1</sup>H NMR spectra of MEEAA functionalized NCs in MeOD after addition of 1.3 equivalents of PA-PEG. Signals arising from bound MEEAA are denoted in red, signals arising from PA-PEG are denoted in striped blue. CNC = 1210 µmol.L<sup>-1</sup>, corresponding to 34 mg NCs of this size in 0.5 ml MeOD. Resonances denoted as * are unidentified impurities.</p> <p><strong>3. Figure 3.pxp</strong>: Experimental data for <em>Figure 3. </em>Diffusion filtered <sup>1</sup>H NMR spectrum of the NC suspension in MeOD at 1.3 equivalents PA-hex-PEG added.</p> <p><strong>4. Figure 4.pxp</strong>: Experimental data for <em>Figure 4.</em> (A) and (B) <sup>31</sup>P NMR spectra of PA-PEG and PA-hex-PEG functionalized NCs at different D<sub>2</sub>O volume %. (C) Free ligand fraction for PA-PEG and PA-hex-PEG at different D<sub>2</sub>O volume %, determined by peak deconvolution.</p> <p><strong>5. Figure 5.pxp</strong>: Experimental data for <em>Figure 5.</em> (A) Ligand exchange performed between MEEAA functionalized NCs and nitrodopamine-mPEG. (B) <sup>1</sup>H NMR spectra before and after the ligand exchange titration performed in D<sub>2</sub>O with nitrodopamine-mPEG. 1.5 equivalents of nitrodopamine-mPEG were added and the pH was kept above 5 at all times during addition, the purified nitrodopamine functionalized NC spectrum was measured at pH = 7.4. CNC = 128 µmol.L<sup>-1</sup>, corresponding to 14.4 mg NCs of this size in 2 ml D<sub>2</sub>O.</p> <p><strong>6. Figure 6.pxp</strong>: Experimental data for <em>Figure 6. </em>Effect of pH on ligand binding and stability in water for purified NCs functionalized with PA-PEG, PA-hex-PEG and nitrodopamine-mPEG. (A) Bound and unbound ligand fraction in D<sub>2</sub>O based on NMR peak deconvolution at different pH values. (B) Z-average value of NCs in DLS at different pH values. (C) Zeta potential of the NCs at different pH values. All measurements were performed at constant ionic strength (0.01 mol.L<sup>-1</sup> NaCl) at 25°C</p> <p><strong>7. Figure 7.pxp</strong>: Experimental data for <em>Figure 7.</em> Stability of functionalized NCs in different concentrations of phosphate buffered saline (PBS) at pH 7.4 and 25°C. (A) Colloidal stability of functionalized nanocrystals measured using DLS z-average values at different PBS concentrations. (B) Stability of functionalized NCs in 2X PBS over time at pH 7.4 and 25°C.</p> <p><strong>8. Figure 9.pxp</strong>: Experimental data for <em>Figure 9.</em> UV-VIS spectra of purified nitrodopamine-mPEG functionalized NCs at different pH values in H2O.</p> <p> </p>
Characterizing the consensus residue specificity and surface of Bcl-2 binding to BH3 ligands using the knob-socket model
<p><span>Cancer cells bypass cell death by changing the expression of the BCL-2 family of proteins, which are apoptotic pathway regulators. Upregulation of pro-survival BCL-2 proteins or downregulation of cell death effectors BAX and BAK interferes with the initiation of the intrinsic apoptotic pathway. In normal cells, apoptosis can occur through pro-apoptotic BH3-only proteins interacting and inhibiting pro-survival BCL-2 proteins. When cancer cells over-express pro-survival BCL-2 proteins, a potential remedy is the sequestration of these pro-survival proteins through a class of anti-cancer drugs called BH3 mimetics that bind in the hydrophobic groove of pro-survival BCL-2 proteins. To improve the design of these BH3 mimetics, the packing interface between BH3 domain ligands and pro-survival BCL-2 proteins was analyzed using the Knob-Socket model to identify the amino acid residues responsible for interaction affinity and specificity. A Knob-Socket analysis organizes all the residues in a binding interface into simple 4 residue units: 3-residue sockets defining surfaces on a protein that pack a 4th residue knob from the other protein. In this way, the position and composition of the knobs packing into sockets across the BH3/BCL-2 interface can be classified. A Knob-Socket analysis of 19 BCL-2 protein and BH3 helix co-crystals reveal multiple conserved binding patterns across protein paralogs. Conserved knob residues such as a Gly, Leu, Ala and Glu most likely define binding specificity in the BH3/BCL-2 interface, whereas other residues such as Asp, Asn, and Val are important for forming surface sockets that bind these knobs. These findings can be used to inform the design of BH3 mimetics that are specific to pro-survival BCL-2 proteins for cancer therapeutics.</span></p>
Characterizing the consensus residue specificity and surface of Bcl-2 binding to BH3 ligands using the knob-socket model
Open the record for dataset details and reuse information.
A Universal Database of Surface Ligands for Quantum Dots
<p>We introduce a public database of organic molecules, derived by an advanced filtering of the PUBCHEM database, with the aim of building a subset of surface ligands candidates that are potentially suitable to passivate the surface of any colloidal QD. For each ligand in the database, we additionally provide relevant chemical and physical properties, from the boiling and melting points to more specific properties that account for the interactions with the solvent and amongst ligands themselves at the QD surface.</p> <div> </div> <p>The “smiles to filter” scanning process, excluding (or including) a set of molecules based on structural characteristics like their functional groups was performed using the Python-based library <a href="https://github.com/nlesc-nano/flamingo">Flamingo</a>. The estimation of COSMO-RS (COnductor-like Screening MOdel for Realistic Solvents) [2] properties was carried out by the Fast Sigma program implemented in AMS (Amsterdam Modelling Suite) [3]. The calculations were automatized and managed via the Compound Attachment Tools (<a href="https://github.com/nlesc-nano/CAT">CAT</a>) [4] and sister packages <a href="https://github.com/nlesc-nano/nano-CAT">nano-CAT</a> and <a href="https://github.com/nlesc-nano/data-CAT">data-CAT</a>. The calculations of the cone angle are currently performed via the <a href="https://github.com/nlesc-nano/nano-CAT">nano-CAT</a> code and preceded by a biased conformational search implemented in <a href="https://github.com/nlesc-nano/CAT">CAT</a> and by a geometry optimization at the DFTB level of theory with the GFN1-xTB parameter set [5] using AMS and will be progressively added to the dataset as they become available.</p> <p>[1] Kim S et al., Nucleic Acids Res., 49(D1):D1388–D1395, 2021.</p> <p>[2] Klamt A. et al., J. Phys. Chem., 99(7) : 2224–2235, 1995.</p> <p>[3] te Velde G. et al., J. Comput. Chem., 22(9): 931–967, 2001.</p> <p>[4] van Beek B. et al., J. Chem. Inf. Model. 2022, 62, 22, 5525–5535.</p> <p>[5] Grimme S. et al., J. Chem. Theory Comput., 13(5):1989–2009, 2017.</p> <div> </div> <div> </div>
Next Generation Sequencing of bacterial surface-displayed ENAH EVH1 ligand peptides after a FACS titration sort (MassTitr)
GEO Series GSE166938. Escherichia coli. 97 samples. Type: Other.
Wnt ligands from the embryonic surface ectoderm regulate bimetallic strip optic cup morphogenesis in the mouse
GEO Series GSE65154. Mus musculus. 8 samples. Type: Expression profiling by array.
High-throughput diversification of protein-ligand surfaces to discover chemical inducers of proximity
GEO Series GSE278582. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
Comparison of murine whole gene expression on ligand immobilized surfaces
GEO Series GSE62304. Mus musculus. 5 samples. Type: Expression profiling by array.
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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.