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418 results for “Dimerization”
Structural models and Sort-seq data for: Packing of apolar amino acids is not a strong stabilizing force in transmembrane helix dimerization
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Data from: Brucella NyxA and NyxB dimerization enhances effector function during infection
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Data for: The conserved centrosomin motif, γTuNA, forms a dimer that directly activates microtubule nucleation by the γ-tubulin ring complex (γTuRC)
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Measurement of biochemical Marker Dynamics in serum levels of calcium, phosphorus, P1NP, and CTX across three time points (T0, T1, T2) following treatment with dimeric R25CPTH(1-34), rhPTH(1-34), and control
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High-throughput discovery of transmembrane helix dimers from human single-pass membrane proteins with TOXGREEN sort-seq
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Data from: A monomer-dimer switch modulates the activity of plant adenosine kinase
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Data from: Conditional requirement for dimerization of the membrane-binding module for BTK signaling in lymphocyte cell lines
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Key features of inhibitor binding to the human mitochondrial pyruvate carrier hetero-dimer
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Data from: Nanomechanics of wild-type and mutant dimers of the tip-link protein protocadherin 15
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Blood test dynamics in hospitalized COVID-19 patients: potential utility of D-dimer for pulmonary embolism diagnosis
<p>SPSS dataset with metadata of the published article in PlosOne and MedRxIv</p>
Simulations of GpA-based dimers of various lengths in DEPC, DOPC, and DLPC bilayers, part 2/2
<p>Dimers of transmembrane (TM) peptides based on the Glycophorin A (GpA) dimer are simulated in different membrane environments. Three different homodimers with varying TM domain lengths and one heterodimer are considered. The homodimers are formed of either</p> <ul> <li>17L (GRPNLKLLL<strong>GV</strong>LL<strong>GV</strong>LL<strong>T</strong>LLLLEYP)</li> <li>23L (GRPNLKLLLLLL<strong>GV</strong>LL<strong>GV</strong>LL<strong>T</strong>LLLLLLLEYP)</li> <li>29L (GRPNLKLLLLLLLLL<strong>GV</strong>LL<strong>GV</strong>LL<strong>T</strong>LLLLLLLLLLEYP)</li> </ul> <p>peptides, while the heterodimer consists of one 17L peptide and one 29L peptide. In the sequences, the bold letters denote the amino acids involved in the GpA dimerization motif. The dimers are simulated in DLPC (12:0 PC), DOPC (18:1 PC), or DEPC (22:1 PC) bilayers. Additionally, a polyleucine dimer is simulated in a DOPC bilayer. Bilayers consist of 400 lipids and they are adequately hydrated with 24000 water molecules and 134 mM NaCl. The simulations are 100 ns long with trajectories written every 100 ps.</p> <p>The files are named as XXX-YYYY.ZZZ, where XXX denotes to the peptide type ('het' for the heterodimer and 'polyl' for the polyleucine), YYYY denotes the bilayer type, and ZZZ denotes the file type. Files are in Gromacs format: .xtc for trajectories, .edr for energy data, .cpt for continue points, .ndx for index files, .top for topology files, and .tpr for run input files (Gromacs 5.1). The simulation parameter file (md.mdp) is common for all systems. The CHARMM36 force field is used; topologies are obtained from CHARMM-GUI, and those of the peptides are included in Gromacs format (.itp).</p> <p>More information on the systems is available in the publication, available here: (TO BE INCLUDED!)</p> <p>Note that the data for the homodimers (bar polyleucine) are in part 1/2, available at https://doi.org/10.5281/zenodo.573257</p>
Simulations of GpA-based dimers of various lengths in DEPC, DOPC, and DLPC bilayers, part 1/2
<p>Dimers of transmembrane (TM) peptides based on the Glycophorin A (GpA) dimer are simulated in different membrane environments. Three different homodimers with varying TM domain lengths and one heterodimer are considered. The homodimers are formed of either</p> <ul> <li>17L (GRPNLKLLL<strong>GV</strong>LL<strong>GV</strong>LL<strong>T</strong>LLLLEYP)</li> <li>23L (GRPNLKLLLLLL<strong>GV</strong>LL<strong>GV</strong>LL<strong>T</strong>LLLLLLLEYP)</li> <li>29L (GRPNLKLLLLLLLLL<strong>GV</strong>LL<strong>GV</strong>LL<strong>T</strong>LLLLLLLLLLEYP)</li> </ul> <p>peptides, while the heterodimer consists of one 17L peptide and one 29L peptide. In the sequences, the bold letters denote the amino acids involved in the GpA dimerization motif. The dimers are simulated in DLPC (12:0 PC), DOPC (18:1 PC), or DEPC (22:1 PC) bilayers. Additionally, a polyleucine dimer is simulated in a DOPC bilayer. Bilayers consist of 400 lipids and they are adequately hydrated with 24000 water molecules and 134 mM NaCl. The simulations are 100 ns long with trajectories written every 100 ps.</p> <p>The files are named as XXX-YYYY.ZZZ, where XXX denotes to the peptide type ('het' for the heterodimer and 'polyl' for the polyleucine), YYYY denotes the bilayer type, and ZZZ denotes the file type. Files are in Gromacs format: .xtc for trajectories, .edr for energy data, .cpt for continue points, .ndx for index files, .top for topology files, and .tpr for run input files (Gromacs 5.1). The simulation parameter file (md.mdp) is common for all systems. The CHARMM36 force field is used; topologies are obtained from CHARMM-GUI, and those of the peptides are included in Gromacs format (.itp).</p> <p>More information on the systems is available in the publication, available here: (TO BE INCLUDED!)</p> <p>Note that the data for the heterodimer and for the polyleucine are in part 2/2, available at https://doi.org/10.5281/zenodo.573274</p>
Dataset of light microscopy and image processing for ruthenium red staining - Rhamnogalacturonan-II dimerization deficiency impairs the coordination between growth and adhesion maintenance in plants
<p>This contains additional data relative to version 1, corresponding to a new versio of the manuscript. </p> <p>This dataset contains darkfield light microscopy images from ruthenium red stained <em>Arabidopsis thaliana </em>dark grown hypocotyls of various wildtype and mutant plants, along with the prossessing and quantified data (including segmented masks, corrected masks, raw quantification and processed quantification) reported in the study "Rhamnogalacturonan-II dimerization deficiency impairs the coordination between growth and adhesion maintenance in plants" (<a href="https://www.biorxiv.org/content/10.1101/2024.11.26.625362v1">https://www.biorxiv.org/content/10.1101/2024.11.26.625362v1</a>). Data was acquired following the method described in the publication. Processing of the raw data was perfomed using the RRQuant workflow (<a href="https://doi.org/10.5281/zenodo.14173186">10.5281/zenodo.14173186</a>).</p>
Dataset and code from tensile test experiments - Rhamnogalacturonan-II dimerization deficiency impairs the coordination between growth and adhesion maintenance in plants
<p>This data set contains brightfield light microscopy images, extensometer reading and other measurments associated with tensile test experiment performed on <em>Arabidopsis thaliana </em>dark grown hypocotyls of various wildtype and mutant plants, along with the prossessing and quantified data as reported in the study "Rhamnogalacturonan-II dimerization deficiency impairs the coordination between growth and adhesion maintenance in plants" (<a href="https://www.biorxiv.org/content/10.1101/2024.11.26.625362v1">https://www.biorxiv.org/content/10.1101/2024.11.26.625362v1</a>). Data was acquired following the method described in the publication. Processing of the raw data was perfomed using the RRQuant workflow (<a href="https://doi.org/10.5281/zenodo.14173186">10.5281/zenodo.14173186</a>).</p>
NMR spectra of single-stranded and dimeric oligonucleotide constructs containing oxidative lesions
<p>NMR spectra of single-stranded (g- prefix) and dimeric (m- prefix) oligonucleotide constructs containing 8-oxoguanine (X) and dSpacer (S) lesions. Spectra were recorded on 600 and 800 MHz spectrometers. Oligonucleotides were dissolved in 50 mM KCl, 10 mM potassium phosphate buffer at pH 7, in 10% 2H2O.</p>
Computational Data: Accurately computed dimerization trends of ALD precursors and their impact on surface reactivity in area-selective atomic layer deposition
<p><span>The Lewis acidic nature of aluminum atoms in common precursors for the atomic layer deposition (ALD) of Al<sub>2</sub>O<sub>3</sub> can lead to dimerization. This study investigates whether these compounds predominantly exist as monomers or dimers under ALD conditions. Understanding dimerization is crucial for discussing precursor reactivities and other properties, especially in the context of area-selective ALD (AS-ALD). We employed a theoretical approach, incorporating conformer search, density functional theory, and coupled cluster calculations, to determine the dissociated dimer fraction for a range of precursors under typical ALD pressures and temperatures. The precursors studied include aluminum alkyls, chlorinated aluminum alkyls, dimethylaluminumisopropoxide (DMAI), and trisdimethylamidoaluminum (TDMAA). Our findings indicate that aluminum alkyls are completely dissociated over the whole parameter range, while DMAI and TDMAA form stable dimers. Chlorinated precursors were found to exist in both monomeric and dimeric forms depending on temperature and pressure.</span></p>
Amyloid-beta 16-22 peptide dimer simulation (150 mM NaCl) with the CHARMM-Drude force field and OpenMM (Run 2)
<p>MD simulations of the Amyloid-beta 16-22 dimer at 150 mM NaCl concentration with CHARMM-Drude force field and OpenMM. Initial structure is obtained from CHARMM-GUI. In the initial configuration, two amyloid-beta 16-22 monomers are not interacting. This repository contains the second out of three independent runs.</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with OpenMM v. 7.5.1.</p> <p>The trajectory is divided into 7 parts: part_1-2 are each 200 ns long; part_3-6 are each 100 ns long, and part_7 is 640 ns long. Frames are saved in every 10 ps.</p>
Amyloid-beta 16-22 peptide dimer simulation (150 mM NaCl) with the CHARMM-Drude force field and OpenMM (Run 1)
<p>MD simulations of the Amyloid-beta 16-22 dimer at 150 mM NaCl concentration with CHARMM-Drude force field and OpenMM. Initial structure is obtained from CHARMM-GUI. In the initial configuration, two amyloid-beta 16-22 monomers are not interacting. This repository contains the first out of three independent runs.</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with OpenMM v. 7.5.1.</p> <p>The trajectory is divided into 7 parts: part_1-2 are each 200 ns long; part_3-6 are each 100 ns long, and part_7 is 640 ns long. Frames are saved in every 10 ps.</p>
Amyloid-beta 16-22 peptide dimer simulation (150 mM NaCl) with the CHARMM-Drude force field and OpenMM (Run 3)
<p>MD simulations of the Amyloid-beta 16-22 dimer at 150 mM NaCl concentration with CHARMM-Drude force field and OpenMM. Initial structure is obtained from CHARMM-GUI. In the initial configuration, two amyloid-beta 16-22 monomers are not interacting. This repository contains the third out of three independent runs.</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with OpenMM v. 7.5.1.</p> <p>The trajectory is divided into 7 parts: part_1-2 are each 200 ns long; part_3-6 are each 100 ns long, and part_7 is 640 ns long. Frames are saved in every 10 ps.</p>
Amyloid-beta 16-22 peptide dimer simulation (150mM NaCl) with the CHARMM36m force field and Gromacs (Run 2)
<p>Amyloid-beta 16-22 peptide dimer simulation with the CHARMM36m force field. This directory contains the second of the three independent trajectories and the simulation length is 1 microseconds. The system contains two amyloid-beta 16-22 monomers, 30 Na+, 30 Cl-, and 10564 TIP3P water.</p>
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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.