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14 results for “ion selectivity”
A Data Set of 255,000 Randomly Selected and Manually Classified Extracted Ion Chromatograms for Evaluation of Peak Detection Methods
<p>Non-targeted mass spectrometry (MS) has become an important method over the last years in the fields of metabolomics and environmental research. While more and more algorithms and workflows become available to process a large number of data sets nontargeted, there still exist few manually evaluated universal test data sets for refining and evaluating these methods. The first step of non-targeted screening, peak detection (and refinement of it) is arguably the most important step for non-targeted screening. However, the absence of a model data set makes it harder for researchers to evaluate peak detection methods. In this Data Descriptor, we provide a manually checked data set consisting of 255,000 EICs (5000 peaks randomly sampled from across 51 samples) for the evaluation on peak detection and gap filling algorithms. The data set was created from a previous real-world study, of which a subset was used to extract and manually classify ion chromatograms by three mass spectrometry experts. The data set consists of:</p> <ul> <li>51 converted mass spectral files in mzML format</li> <li>An .RData-file containing the extracted ion chromtograms (EICs)</li> <li>The randomly selected subset and the original output table of MZmine in .csv-format</li> <li>Example .xlsx files for the classification</li> <li>2 central classification tables</li> <li>Several tables with additional information about the sampling, chemical analysis and expert jugdement on EICs</li> </ul> <p>For a full description of the experiment and the data set, please read the related Data Descriptor with the title "A data set of 255000 randomly selected and manually classified extracted ion chromatograms for evaluation of peak detection methods" in Metabolites (https://www.mdpi.com/journal/metabolites; DOI: https://doi.org/10.3390/metabo10040162).</p>
Optimized geometries for selected ions of ionic liquids and small molecules
<p>The geometries of these selected chemical entities were optimized at the ab initio or semiempirical levels of theory. They can be conveniently used to create more complicated systems through combining species like the free PACKMOL software offers. </p>
Porous Organic Polymers with Heterocyclic Crown Ethers for Selective Lithium-Ion Capture
<p>Abstract of the publication: Lithium is a key resource of the 21st century. Despite that, Li is traditionally mined rather than obtained from maritime brines or secondary sources such as spent energy-storage devices owing to the difficulties in Li recovery. Herein, we present a porous organic polymer capable of capturing Li ions from aqueous solutions through highly pre-organized heterocyclic crown ether-like pores in the polymer backbone. These features enable Li+ uptake capacities over 120 mg g-1 and selectivity versus highly competitive ions such as Na+, Ca2+, and Mg2+.</p> <p> </p>
Square Antiprismatic Ion Chelation Is a Key Determinant for Potassium Channel Selectivity
<p>Files presented here are archives K_DB.tar.gz, MEMB_DB.tar.gz and PDB70.tar.gz.</p> <p>Archives KDB.tar.gz, MEMB_DB.tar.gz and PDB70.tar.gz contain models of indentified sites for potassium channels (dataset #1), other membrane proteins, excluding potassium channels (dataset #2) and non-membrane proteins form PDB70 (dataset #3). The name of a folder in the dataset corresponds to PDB ID of a protein for which calculation were made. Each folder contain the following files:</p> <ul> <li><PDB_ID>.pdb — the original pdb file.</li> <li><PDB_ID>.ref — file that contains oxygens and nitrogens from original pdb that were used for scanning.</li> <li><PDB_ID>_COMBS.txt — combinations of atoms that were used for calculations.</li> <li><PDB_ID>_alignment_X.pdb — original template that was aligned to the protein atoms. X denotes a number of the alignment.</li> <li><PDB_ID>_site_X.pdb — this pdb file contains eight atoms that form the site for K+ and which were used for the corresponding alignment X.</li> <li><PDB_ID>_RES.txt — the combinations of protein atoms that form the site are written in square brackets. The RMSD value for the alignment to this site is written to the right of them.</li> <li><PDB_ID>_RMSD.log — this file contains RMSD values of the template alignment to the corresponding site.</li> </ul>
Square Antiprismatic Chelation Is a Key Determinant for Potassium Ion Selectivity
<p><strong>DATASETS</strong></p> <p>Archives <em>K_DB.tar.gz</em>, <em>MEMB_DB.tar.gz</em> and <em>PDB70.tar.gz</em> contain models of indentified sites for potassium channels (dataset #1), other membrane proteins, excluding potassium channels (dataset #2) and non-membrane proteins form PDB70 (dataset #3). The name of a folder in the dataset corresponds to PDB ID of a protein for which calculation were made. Each folder contain the following files:</p> <ul> <li><PDB_ID>.pdb — the original pdb file.</li> <li><PDB_ID>.ref — file that contains oxygens and nitrogens from original pdb that were used for scanning.</li> <li><PDB_ID>_COMBS.txt — combinations of atoms that were used for calculations.</li> <li><PDB_ID>_alignment_X.pdb — original template that was aligned to the protein atoms. X denotes a number of the alignment.</li> <li><PDB_ID>_site_X.pdb — this pdb file contains eight atoms that form the site for K+ and which were used for the corresponding alignment X.</li> <li><PDB_ID>_RES.txt — the combinations of protein atoms that form the site are written in square brackets. The RMSD value for the alignment to this site is written to the right of them.</li> <li><PDB_ID>_RMSD.log — this file contains RMSD values of the template alignment to the corresponding site.</li> </ul> <p><strong>SUPPLEMENTARY TABLES S1-S5</strong></p> <p>The file <em>Supporting Information_Tables S1-S5.xlsx </em>contain tables S1-S5 for the supporting information from the original paper. These tables describe potassium binding sites indentifieid in potassium channels, other membrane proteins and randomly chosen non-membrane proteins. (See the article text for details)</p> <p> </p> <p> </p>
Data for: In situ generation of (sub) nanometer pores in MoS2 membranes for ion-selective transport
<p>Source data for Fig 1-3 includes data for ion transport measurements and pore size distributions.</p> <p>Source data for Fig. 4 includes trajectory data for molecular dynamics simulations, exclusively for ions within MoS2 nanopores, as well as full trajectory data for the calculation of water-diffusion in 1 nm, 2 nm pores and the bulk reservoir (without an applied electric field). </p>
Rational Material Selection for Li-Ion-Based Thermogalvanic Harvesting Devices
<p>This dataset contains the raw data for the publication "Rational Material Selection for Li-Ion-Based Thermogalvanic Harvesting Devices" by Hubrechtsen et al, published in Chemistry of Materials. The upload includes all data for the original figures presented in the main paper and the supporting information, organized in labelled folders containing raw data and the corresponding figure. </p>
Supplementary Tables S1-S5 for an article "Square Antiprismatic Chelation Is a Key Determinant for Potassium Ion Selectivity"
<p>This file contain tables S1-S5 for the supporting information from the original paper. These tables describe potassium binding sites indentifieid in potassium channels, other membrane proteins and randomly chosen non-membrane proteins. (See the article text for details)</p> <p> </p>
Square Antiprismatic Chelation Is a Key Determinant for Potassium Ion Selectivity
<p><strong>DATASETS</strong></p> <p>Archives <em>K_DB.tar.gz</em>, <em>MEMB_DB.tar.gz</em> and <em>PDB70.tar.gz</em> contain models of indentified sites for potassium channels (dataset #1), other membrane proteins, excluding potassium channels (dataset #2) and non-membrane proteins form PDB70 (dataset #3). The name of a folder in the dataset corresponds to PDB ID of a protein for which calculation were made. Each folder contain the following files:</p> <ul> <li><PDB_ID>.pdb — the original pdb file.</li> <li><PDB_ID>.ref — file that contains oxygens and nitrogens from original pdb that were used for scanning.</li> <li><PDB_ID>_COMBS.txt — combinations of atoms that were used for calculations.</li> <li><PDB_ID>_alignment_X.pdb — original template that was aligned to the protein atoms. X denotes a number of the alignment.</li> <li><PDB_ID>_site_X.pdb — this pdb file contains eight atoms that form the site for K+ and which were used for the corresponding alignment X.</li> <li><PDB_ID>_RES.txt — the combinations of protein atoms that form the site are written in square brackets. The RMSD value for the alignment to this site is written to the right of them.</li> <li><PDB_ID>_RMSD.log — this file contains RMSD values of the template alignment to the corresponding site.</li> </ul> <p><strong>SUPPLEMENTARY TABLES S1-S5</strong></p> <p>The file <em>Supporting Information_Tables S1-S5.xlsx </em>contain tables S1-S5 for the supporting information from the original paper. These tables describe potassium binding sites indentifieid in potassium channels, other membrane proteins and randomly chosen non-membrane proteins. (See the article text for details)</p> <p> </p>
Data from Selectivity filter mutations shift ion permeation mechanism in potassium channels
<p>Example mdp, gro files, topologies, scripts, run input files and trajectories used in https://doi.org/10.1101/2023.04.17.537168</p>
Data from: Positive selection on sperm ion channels in a brooding brittle star: consequence of life-history traits evolution
Open the record for dataset details and reuse information.
Square Antiprismatic Chelation Is a Key Determinant for Potassium Ion Selectivity
<p>Files presented here are archives KDB.tar.gz, MEMB_DB.tar.gz and PDB70.tar.gz.</p> <p>Archives KDB.tar.gz, MEMB_DB.tar.gz and PDB70.tar.gz contain models of indentified sites for potassium channels (dataset #1), other membrane proteins, excluding potassium channels (dataset #2) and non-membrane proteins form PDB70 (dataset #3). The name of a folder in the dataset corresponds to PDB ID of a protein for which calculation were made. Each folder contain the following files:</p> <ul> <li><PDB_ID>.pdb — the original pdb file.</li> <li><PDB_ID>.ref — file that contains oxygens and nitrogens from original pdb that were used for scanning.</li> <li><PDB_ID>_COMBS.txt — combinations of atoms that were used for calculations.</li> <li><PDB_ID>_alignment_X.pdb — original template that was aligned to the protein atoms. X denotes a number of the alignment.</li> <li><PDB_ID>_site_X.pdb — this pdb file contains eight atoms that form the site for K+ and which were used for the corresponding alignment X.</li> <li><PDB_ID>_RES.txt — the combinations of protein atoms that form the site are written in square brackets. The RMSD value for the alignment to this site is written to the right of them.</li> <li><PDB_ID>_RMSD.log — this file contains RMSD values of the template alignment to the corresponding site.</li> </ul> <p> </p>
Square Antiprismatic Chelation Is a Key Determinant for Potassium Ion Selectivity
<p>Files presented here are archives KDB.tar.gz, MEMB_DB.tar.gz and PDB70.tar.gz.</p> <p>Archives KDB.tar.gz, MEMB_DB.tar.gz and PDB70.tar.gz contain models of indentified sites for potassium channels (dataset #1), other membrane proteins, excluding potassium channels (dataset #2) and non-membrane proteins form PDB70 (dataset #3). The name of a folder in the dataset corresponds to PDB ID of a protein for which calculation were made. Each folder contain the following files:</p> <ul> <li><PDB_ID>.pdb — the original pdb file.</li> <li><PDB_ID>.ref — file that contains oxygens and nitrogens from original pdb that were used for scanning.</li> <li><PDB_ID>_COMBS.txt — combinations of atoms that were used for calculations.</li> <li><PDB_ID>_alignment_X.pdb — original template that was aligned to the protein atoms. X denotes a number of the alignment.</li> <li><PDB_ID>_site_X.pdb — this pdb file contains eight atoms that form the site for K+ and which were used for the corresponding alignment X.</li> <li><PDB_ID>_RES.txt — the combinations of protein atoms that form the site are written in square brackets. The RMSD value for the alignment to this site is written to the right of them.</li> <li><PDB_ID>_RMSD.log — this file contains RMSD values of the template alignment to the corresponding site.</li> </ul>
Mass spectrometric highly selective, sensitive, accurate and precise quantification of species of zinc(II) ion among other transition metal ions based on coordination with glycylhomopentapeptide – a stochastic dynamic approach - experimental dataset
<p>Experimental dataset of mass spectra of Zn<sup>II</sup>-complexes of a glycylhomooligopeptide </p>
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Allen Brain Atlas
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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.
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