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873 results for “ligands”
AutoDock and CB-Dock data for (NPA)6Zn3(H2O)2 in Synthesis, structural analysis, and docking studies with SARS-CoV-2 of a trinuclear zinc complex with N-phenylanthranilic acid ligands
<p>AutoDock 4.2 and CB-Dock data for (NPA)<sub>6</sub>Zn<sub>3</sub>(H<sub>2</sub>O)<sub>2</sub> with M<sup>pro</sup> from SARS-CoV-2 from PDB Id: 6LU7. </p>
NMR data for (NPA)6Zn3(H2O)2 in Synthesis, structural analysis, and docking studies with SARS-CoV-2 of a trinuclear zinc complex with N-phenylanthranilic acid ligands
<p><sup>1</sup>H, <sup>13</sup>C, COSY, HMBC, and HSQC NMR data in fid format for (NPA)<sub>6</sub>Zn<sub>3</sub>(H<sub>2</sub>O)<sub>2</sub> (NPA = 2-(phenylamino) benzoate) in DMSO-<em>d</em><sub>6.</sub></p>
Dataset Klussmeier et al., Secretin receptor as a target in gastrointestinal cancer: expression analysis and ligand development
<p>Numerical dataset for the manuscript by Klussmeier et al., Secretin receptor as a target in gastrointestinal cancer: expression analysis and ligand development.</p>
Sampled ΔH/Δλ and ΔH data from ABFE calculations of 19 ligands bound to MCL-1
<p>Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process"</p> <p>Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 19 ligands to bound MCL-1. These ligands are originally detailed by Friberg et al. (https://doi.org/10.1021/jm301448p).</p> <p>All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information.</p> <p>Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders).</p> <p>Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).</p>
Sampled ΔH/Δλ and ΔH data from ABFE calculations (using standard atomic masses) of 10 ligands bound to Cyclophilin D
<p>Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process"</p> <p>Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 10 ligands to bound Cyclophilin D. These ligands are originally detailed by Grädler et al. (https://doi.org/10.1016/j.bmcl.2019.126717). Unlike other datasets in this work, which employed hydrogen mass repartitioning, the ligands here were calculated using standard atomic masses.</p> <p>All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information.</p> <p>Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders).</p> <p>Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).</p>
Sampled ΔH/Δλ and ΔH data from ABFE calculations of 12 ligands bound to PWWP1
<p>Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process"</p> <p>Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 12 ligands to bound PWWP1. These ligands are originally detailed by Böttcher et al. (https://doi.org/10.1038/s41589-019-0310-x).</p> <p>All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information.</p> <p>Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders).</p> <p>Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).</p>
Sampled ΔH/Δλ and ΔH data from ABFE calculations of 10 ligands bound to Cyclophilin D
<p>Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process"</p> <p>Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 10 ligands bound to Cyclophilin D. These ligands are originally detailed by Grädler et al. (https://doi.org/10.1016/j.bmcl.2019.126717). Unlike the other Cyclophilin D<br> dataset provided in this work, simulations for these ABFE calculations were carried out using hydrogen mass repartitioning (HMR). The MCL-1, HSP90, and PWWP1 also used HMR.</p> <p>All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information.</p> <p>Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders).</p> <p>Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).<br> </p>
Sampled ΔH/Δλ and ΔH data from ABFE calculations of 18 ligands bound to HSP90
<p>Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process"</p> <p>Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 18 ligands bound to HSP90. These ligands are originally detailed by Murray et al. (https://doi.org/10.1021/jm100059d).</p> <p>All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information.</p> <p>Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders).</p> <p>Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).</p>
Colloidal-ALD Grown Hybrid Shells Nucleate via a Ligand–Precursor Complex
<p>Colloidal atomic layer deposition (c-ALD) enables the growth of hybrid organic–inorganic oxide shells with tunable thickness<br> at the nanometer scale around ligand-functionalized inorganic nanoparticles (NPs). This recently developed method has demonstrated improved stability of NPs and of their dispersions, a key requirement for their application.<br> Nevertheless, the mechanism by which the inorganic shells form is still unknown, as is the nature of multiple complex interfaces between the NPs, the organic ligands functionalizing the surface, and the shell. Here, we demonstrate that carboxylate ligands are the key element that enables the synthesis of these core–shell structures. Dynamic nuclear polarization surface-enhanced nuclear magnetic resonance spectroscopy (DNP SENS) in combination with density functional theory (DFT) structure calculations shows that the addition of the aluminum organometallic precursor forms a ligand–precursor complex that interacts with the NP surface. This ligand–precursor complex is the first step for the nucleation of the shell and enables its further growth.</p>
PSnpBind: A database of mutated binding site protein-ligand complexes constructed using a multithreaded virtual screening workflow
<p>A key concept in drug design is how natural variants, especially the ones occurring in the binding site of drug targets, affect the inter-individual drug response and efficacy by altering binding affinity. These effects have been studied on very limited and small datasets while, ideally, a large dataset of binding affinity changes due to binding site single-nucleotide polymorphisms (SNPs) is needed for evaluation. However, to the best of our knowledge, such a dataset does not exist. Thus, a reference dataset of ligands binding affinities to proteins with all their reported binding sites’ variants was constructed using a molecular docking approach. Having a large database of protein-ligand complexes covering a wide range of binding pocket mutations and a large small molecules’ landscape is of great importance for several types of studies. For example, developing machine learning algorithms to predict protein-ligand affinity or a SNP effect on it requires an extensive amount of data. In this work, we present PSnpBind: A large database of mutated binding site protein-ligand complexes constructed using a multithreaded virtual screening workflow. It provides a web interface to explore and visualize the protein-ligand complexes and a REST API to programmatically access the different aspects of the database contents. PSnpBind is freely available at <a href="https://psnpbind.org">https://psnpbind.org</a>.<strong> </strong>The source code of the tools used in constructing PSnpBind is available on <a href="https://github.com/ammar257ammar/PSnpBind-Build">GitHub</a>.</p>
X-Ray Structures of Target-Ligand Complexes Containing Compounds with Assay Interference Potential
<p>A total of 2755 crystallographic complexes with ligands containing PAINS-defining substructures were extracted from the Protein Data Bank (PDB). PDB identifiers of these structures are made available together with the the corresponding PDB_PAINS (component identifier, aromatic nonstereo SMILES, PAINS class). </p>
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>
Compilation of Fe and ligand data along the West coast of the United States
<p>Compilation of Fe and ligand data along the West coast of the United States (Compiled by Anh Le-Duy Pham from current available literature as of April 2024)</p> <p> </p> <p><span>USWC_Iron_Ligand_Compilation.xlsx: an excel file containing all the combined dFe and ligand data</span></p> <p><span>USWC_IronLiganddata.mat: a MATLAB file containing all the combined dFe and ligand data</span></p>
IR data of the compounds published in "Synthesis and Reactivity of Molybdenum and Tungsten Alkyne Complexes Containing 6-Methylpyridine-2-thiolate Ligands"
<p>Here, the uploaded data are associated with the manuscript "Synthesis and Reactivity of Molybdenum and Tungsten Alkyne Complexes Containing 6-Methylpyridine-2-thiolate Ligands," published in Helvetica Chimica Acta under the following DOI: https://doi.org/10.1002/hlca.202100137<br>The .dpt files represent IR spectra of the compounds published in the manuscript. The labeling used consists of two parts, e.g., 1b – ME162, where 1b represents the label of the compound as presented in the manuscript, and ME162 represents the crystallographic label found in the supplementary information (SI).</p>
Spectroscopic data of the compounds published in "The Effect of Selenium-Based Ligands on Tungsten Acetylene Complexes"
<p>Here, the uploaded data are associated with the manuscript "The Effect of Selenium-Based Ligands on Tungsten Acetylene Complexes" published in Inorg. Chem. under the following doi/10.1021/acs.inorgchem.4c01636<br>The .dpt files represent IR spectra of the compounds published in the manuscript. The .scv files represent NMR spectra of the compounds and reactions published in the manuscript.<br>The labeling of the compounds and reactions follows the one in the published manuscript.</p>
Dataset: Ligand Pharmaceuticals Incorporated (LGND) Stock Performance
This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.
Figure 2 in Molecular transduction in receptor-ligand systems by planar electromagnetic fields
Figure 2. TCR(αβ) molecules in free (a, b, c) and coupled (d) states, showing the charged residues in red for negative charges and blue for positive charges. The fully conserved residues are highlighted in the boxes below each figure. Image records taken from Jmol.
Figure 1 in Molecular transduction in receptor-ligand systems by planar electromagnetic fields
Figure 1. Spatial positions of fully conserved, charged residues and peptide-recognition residues in TCR. These together form a PECC-i by which the signal reaches the ζζ transmembrane dimer domain. Image recordings taken from Jmol.
Figure 3 in Molecular transduction in receptor-ligand systems by planar electromagnetic fields
Figure 3. Some examples of PECC-i present in: calcium-ADP pump (a,b,c); haemoglobin-oxygen (d,e,f); and gp120-CD4 (g,h,i) receptorligand protein systems. Image records taken from Jmol.
Dataset for: Visualization of oxygen vacancies and self-doped ligand holes in La3Ni2O7-δ
<p>This repository contains representative four-dimensional scanning transmission electron microscopy (4D-STEM) datasets supporting the findings in the related paper, <em>Visualization of oxygen vacancies and self-doped ligand holes in La3Ni2O7-δ</em>. (<em>Nature</em> <strong>630</strong>, 847–852 (2024)).</p> <p>Region01 is one of the datasets from the regions with δ~0.04. Region02 is one of the datasets from the regions with δ~0.17. Region03 is one of the datasets from the regions with δ~0.34. </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.