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276 results for “protein domains”
A Laboratory Evaluation of the Humoral Immune Response in Adults and Children to the H1 Hemagglutinin (HA) Stalk Domain and Other Influenza A Virus Protein Epitopes, After Administration of GlaxoSmith
ClinicalTrials.gov study NCT02415842. IPD Sharing: NO. Countries: 1. Publications: 1.
A DUF630 and 632 domains-containing protein, ZmNRL1, acts as a positive regulator of nitrogen stress response in maize
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Data for: A unique C-terminal domain contributes to the molecular function of restorer-of-fertility proteins in plant mitochondria
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Evolutionary assembly of the plant terrestrialization toolkit from protein domains
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Codes and source data files for: Proximity labeling identifies LOTUS domain proteins that promote the formation of perinuclear germ granules in C. elegans
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Data from: Dissection of the role of a SH3 domain in the evolution of binding preference of paralogous proteins
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Amino acid sequences of RWP-RK domain containing proteins used for the construction of phylogenetic tree shown in Fig. 1
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Equilibration simulations of TM domains of Bcl-2 proteins Mcl-1, Bok, and Bax
<p>Input files and final structures (after 1 microsecond) of simulations of Mcl-1, Bax, and Bok transmembrane domains (TMDs) in a POPC membrane. CHARMM36 parameters are used for lipids and proteins and the CHARMM-specific TIP3P model for water. The systems were set up using CHARMM-GUI, and simualted using GROMACS with the simulation parameters recommended for CHARMM (see md.mdp).</p> <p>The simulations are described in detail in the paper [1]. Briefly, the final structures, given as .gro files here, were coarse-grained and used in high-throughput dimerization analyses. The dimer structures were clustered, and the most promising structures were fine-grained, and their stability was evaluated using atomistic simulations.</p> <p>[1] ADD</p>
Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group C2)
<p>Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group C2). The final structure is deposited in the Protein Data Bank under accession code <a href="https://www.ebi.ac.uk/pdbe/entry/pdb/7AV9">7AV9</a>.</p> <p> </p> <p>Additional information:</p> <p>dataset: PHIPA-x1724<br> beamline: Diamond Light Source I04-1<br> visit: nt11175-63<br> date: 16-04-2015<br> Ω Start: 144.0°<br> Ω Osc: 0.12°<br> Ω Overlap: 0°<br> No. Images: 1500<br> Resolution: 1.50Å<br> Wavelength: 0.9173Å<br> Exposure: 0.040s<br> Transmission: 100.00%<br> Beamsize: 60x50μm</p>
Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group P212121)
<p>Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group P212121). The final structure is deposited in the Protein Data Bank under accession code <a href="https://www.ebi.ac.uk/pdbe/entry/pdb/7BBO">7BBO</a>.</p> <p> </p> <p>Additional information:</p> <p>dataset: PHIPA-x1738<br> beamline: Diamond Light Source I04-1<br> visit: nt11175-63<br> date: 16-04-2015<br> Ω Start: 90.0°<br> Ω Osc: 0.12°<br> Ω Overlap: 0°<br> No. Images: 1500<br> Resolution: 1.50Å<br> Wavelength: 0.9173Å<br> Exposure: 0.040s<br> Transmission: 100.00%<br> Beamsize: 60x50μm</p>
Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with H4K5acK8ac
<p>Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with H4K5acK8ac. The final structure is deposited in the Protein Data Bank under accession code <a href="https://www.ebi.ac.uk/pdbe/entry/pdb/7BBP">7BBP</a>.</p> <p> </p> <p>Additional information:</p> <p>dataset: PHIPA-x2179<br> beamline: Diamond Light Source I04-1<br> visit: mx10619-76<br> date: 20-06-2016<br> Ω Start: 216.3°<br> Ω Osc: 0.15°<br> Ω Overlap: 0°<br> No. Images: 1200<br> Resolution: 2.00Å<br> Wavelength: 0.9282Å<br> Exposure: 0.050s<br> Transmission: 100.00%</p>
Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group p21212)
<p>Raw diffraction images of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group p21212). The final structure is deposited in the Protein Data Bank under accession code <a href="https://www.ebi.ac.uk/pdbe/entry/pdb/7AV8">7AV8</a>.</p> <p>Additional information:</p> <p>dataset: PHIPA-x152<br> beamline: Diamond Light Source I04-1<br> visit: mx8421-63<br> date: 02-03-2014<br> Ω Start: 90.0°<br> Ω Osc: 0.10°<br> Ω Overlap: 0°<br> No. Images: 1800<br> Resolution: 1.50Å<br> Wavelength: 0.9200Å<br> Exposure: 0.050s<br> Transmission: 100.00%<br> Beamsize: 60x50μm</p>
Validation of huntingtin domain protein samples mass spectrometry and aggregation assays 20170130
<p>Open lab notebook huntingtin structure function project.<br> </p>
Optimisation of huntingtin domain protein sample buffer conditions 2017/02/01
<p>Open lab notebook huntingtin structure function project.<br> </p>
Supporting data for transmembrane domain self association simulations in "Recalibration of protein interactions in Martini 3"
<p>This repository contains the data of transmembrane helix self-association simulation from "Recalibration of protein interactions in Martini 3". Simulations were run with the Martini 3.0 force field, along with two modified versions of Martini 3.0 in which the well-depth, ε, in the Lennard-Jones potential between all protein and water beads was rescaled by a factor <em>λ</em><sub>PW</sub>, ε in the Lennard-Jones potential between all protein beads was rescaled by a factor <em>λ</em><sub>PP</sub>. The simulation files are kept in one single zip file, which contains trajectories for two protein EphA1 and ErbB1 systems with three versions of force fields. The trajectory files are in xtc format, and are accompanied by a structure in pdb format for system topology and a tpr file to start the simulation. In each version of force field for each protein, name of the files corresponds to that specific umbrella sampling window. Umbrella sampling windows ranges from 0.6 nm to 3.4 nm with a spacing of 0.2 nm. </p>
Protein domain embedding
<p>CATH and ECOD structure embedding computed with a <a href="https://github.com/BorgwardtLab/PST">Protein Language Model</a>. These two datasets were compiled to develop AI/ML methods for structure comparison (Guzenko 2020). Protein structures from both datasets are independent and can be used as training and testing data for ML methods. </p>
Unraveling the Unfolding Mechanism of Pseudoazurin: Insights into Stabilizing Cupredoxin Fold as a Common Domain of Cu-Containing Proteins
<p>This dataset includes molecular dynamics (MD) simulation trajectories and experimental data used in the title named study. The MD trajectories cover simulations of pseudoazurin under various conditions: apo (pH 2, pH 3, pH 7), holo (pH 2, pH 3, pH 7), and explicit water simulations of holo at pH 7. Additionally, the dataset contains raw experimental data, including small-angle neutron scattering (SANS) curves, visible (Vis) absorption spectra, and circular dichroism (CD) spectra. This comprehensive dataset supports the investigation of unfolding mechanism of Pseudoazurin.</p>
Raw data for: Spidroin N-terminal domain forms amyloid-like fibril based hydrogels and provides a protein immobilization platform
<p>Raw data for the article "Spidroin N-terminal domain forms amyloid-like fibril based hydrogels and provides a protein immobilization platform." to be published in Nature communications.</p>
Rapid Flow-Based Synthesis of Post-Translationally Modified Peptides and Proteins: A Case Study on MYC's Transactivation Domain
<p>Raw data for the project "Rapid Flow-Based Synthesis of Post-Translationally Modified Peptides and Proteins: A Case Study on MYC's Transactivation Domain".</p> <p>Manuscript and supporting information available on Chemical Science: <a title="Link to landing page via DOI" href="https://doi.org/10.1039/D4SC00481G">https://doi.org/10.1039/D4SC00481G</a></p>
SASDM85 – GTP-binding domain of Candida albicans Ras-like protein 1 in complex with the guanine nucleotide exchange factor region of cell division control protein 25
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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.