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77 results for “Peptides and proteins”
Chemical modification of proteins by insertion of synthetic peptides using tandem protein trans-splicing
<p>Source data underlying Figs 2c-e, 3c,e-f, 6c,d,f, and Supplementary Figs S1c, S3a, S4c-e,h-j, S5c, S8b, S9d-e, S10d-e, S11d</p>
Supplemental data: Interfering Peptides Targeting Protein-Protein Interactions in the Ethylene Plant Hormone Signaling Pathway as Tools to Delay Plant Senescence
<p>This dataset supplements the chapter "Interfering Peptides Targeting Protein-Protein Interactions in the Ethylene Plant Hormone Signaling Pathway as Tools to Delay Plant Senescence" published in Methods in Molecular Biology. It includes sample files that illustrate data collection and processing outlined in the article.</p>
Molecular dynamics trajectory videos for high-affinity short peptides targeting BamA protein of Candidatus liberibacter asiaticus
<p>Molecular dynamics trajectory videos and trajectory analysis reports for high-affinity short peptides targeting BamA protein of <em>Candidatus</em> liberibacter asiaticus</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>
Molecular Dynamics Dataset - Dynamics of GLP-1R peptide agonist engagement are correlated with kinetics of G protein activation
<p>Molecular dynamics simulations of the glucagon-like peptide receptor (GLP-1R) in complex with Gs protein and four different agonist peptides: GLP-1, exendin-4, oxyntomodulin, and exendin-P5. </p> <p>For each system, the .xtc file is the result of the merging of 4 replicas of 500 ns for a total of 2 microseconds (8 microseconds considering all four GLP-1R complexes). The original MD trajectories have been stripped of water, ions and phosphatidylcholine atoms before the upload. The CHARMM36 force field was used.</p>
Localization files for "Imaging proteins sensitive to direct fusions using transient peptide-peptide interactions"
<p>Localization csv files for super-resolution images taken and analysed for "Imaging proteins sensitive to direct fusions using transient peptide-peptide interactions". Single localizations were processed using the Peak Fit function of the Fiji (Java 8 2017 release) GDSC SMLM plugin, using a signal strength threshold of 30, a minimum photon threshold of 100, and a precision threshold of 15-30 nm (precision threshold used is indicated in the file name). </p>
Strategy of selection and optimization of single domain antibodies targeting the PHF6 linear peptide within the Tau intrinsically disordered protein
<p>Dataset pertaining to Strategy of selection and optimization of single domain antibodies targeting the PHF6 linear peptide within the Tau intrinsically disordered protein</p>
Clinical Safety of a Novel Milk Protein Peptide
ClinicalTrials.gov study NCT01412658. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Phase Ib Trial of Two Folate Binding Protein Peptide Vaccines (E39 and J65) in Breast and Ovarian Cancer Patients
ClinicalTrials.gov study NCT02019524. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Pooled Mutant KRAS-Targeted Long Peptide Vaccine Combined With Nivolumab and Ipilimumab for Patients With Resected Mismatch Repair Protein (MMR-p) Colorectal and Pancreatic Cancer
ClinicalTrials.gov study NCT04117087. IPD Sharing: NO. Countries: 1. Publications: 0.
Hemp Seed Protein and Bioactive Peptides Consumption for Hypertension
ClinicalTrials.gov study NCT03508895. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Evaluation SIHUMI dataset: A sectioning and database enrichment approach for improved peptide spectrum matching in large, genome-guided protein sequence databases
<p>Dataset for evaluation of database sectioning method for generating an enriched database for mass-spectrometry-based proteomic approaches using large databases. Our evaluation demonstrates that this method helps to increase the sensitivity of PSMs while maintaining acceptable FDR statistics. This dataset was acquired from the protein samples containing proteins from eight microorganisms (<em>Anaerostipes caccae, Bacteroides thetaiotaomicron, Bifidobacterium longum, Blautia producta, Clostridium butyricum, Clostridium ramosum, Escherichia coli, Lactobacillus plantarum</em>) that were grown in a bioreactor. The MS-data for this dataset was acquired by Dr. Hettich's group at Oak Ridge National Laboratory, and it was made available by Dr. Nico Jehmlich from Helmholtz Center for Environmental Research through the 3rd International Metaproteome Symposium (<a href="https://www.ufz.de/index.php?en=44639">https://www.ufz.de/index.php?en=44639</a>). </p>
Assessing SIRAH's Capability to Simulate Intrinsically Disordered Proteins and Peptides
<p>This dataset contains the structures, topologies, and trajectory files of coarse-grained molecular dynamics simulations of five Intrinsically Disordered Proteins (IDPs). We explored the dynamics of α-synuclein (randomly generated conformers), p31-43(PDB is: 6QAX), PaaA2 antitoxin (PDB id:3ZBE), Amyloid-beta 1-40 (PDB id: 2FLM), and Insulin C-peptide (PDB id: 1T0C) using the SIRAH force field running with the Gromacs 18.4 under the conditions reported in <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00006">Machado et al. JCTC 2019</a>, adding 150 mM NaCl according to <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953">Machado & Pantano JCTC 2020</a>. Briefly, simulations were performed in triplicate for 5 μs at 300 K and 1 atm in the NPT ensemble. We used a time-step of 20 fs, a direct cutoff for non-bonded interactions of 1.2 nm, and Particle Mesh Ewald summation for long-range electrostatics. For α-synuclein and p31-43, initial conformations were obtained from models built on arbitrary conformations and heated up to 340 K. For PaaA2 antitoxin, Amyloid-beta 1-40, and Proinsulin C-peptide, three different NMR conformers were arbitrarily selected. </p> <p>The information is divided into five tar files containing each system's data (only protein coordinates are reported). Additionally, the Sirah Tools' tcl script with macros for selections and analyses is also included. Please visit http://www.sirahff.com for step-by-step tutorials on running and analyzing CG simulations with SIRAH. </p> <p>To take a quick look at the trajectories:</p> <p>1- Untar the tar file of interest </p> <p>2- Open the trajectory on VMD using the command line:</p> <p>vmd "your_protein".psf "your_protein".xtc -e sirah_vmdtk.tcl</p> <p><br> Note that using the tcl script you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.</p> <p>This dataset contains simulations associated to a manuscript with the same title and by the same authors.</p> <p>For questions, kindly contact Florencia Klein (fklein@pasteur.edu.uy), Exequiel Barrera (ebarrera@pasteur.edu.uy), or Sergio Pantano (spantano@pasteur.edu.uy).</p>
Transmission electron microscopy (TEM) image datasets of peptide / protein nanowire morphologies
<p>TEM image dataset containing four nanowire morphologies of bio-derived protein nanowires and synthetic peptide nanowires.</p> <p>The peptide / protein nanowires used in this study were synthesized and imaged by Brian Montz in Prof. Todd Emrick's research group at the Department of Polymer Science and Engineering Department, University of Massachusetts Amherst. </p> <p>We acknowledge financial support from the U.S. National Science Foundation, Grant NSF DMREF #1921839 and DMREF #1921871.</p> <p>Nanowires were classified into either of the four morphologies: bundle, singular, dispersed or network. Each morphology contains 100 images (jpg files).</p> <p>For the dispersed and network morphologies, because these two morphologies are harder to visually distinguish, we have created manual segmentation labels of the nanowires (included in these two morphology folders as png files). Percolation analysis was done on these manually segmented nanowires to provide quantitative metric on whether the nanowires form a network in the image. </p> <p>seg_mask_5_resolutions.zip contains ground truth 2D binary encoding of segmented nanowires at 5 resolutions.</p> <p>encoders_trained_with_optimized_hyperparameter.zip contains 4 sets of encoders trained with either SimCLR or Barlow-Twins self-supervised methods on either generic TEM images, or generic everyday photographic images (each with 5 replicates with different random seed) with optimized hyperparameters.</p> <p>Open-access datasets that have been used during self-supervised training.</p> <ul> <li>2021-CEM500K.zip contains 10,000 images that was used as "generic TEM images" to train the encoders with self-supervised methods, these are a random selection from the CEM500k open-access dataset. DOI: <a href="https://doi.org/10.7554/eLife.65894">10.7554/eLife.65894</a></li> <li>2022-1000-ImageNet.zip contains 1,000 images from the ImageNet1k dataset, each come from a different category. DOI: <a href="http://doi.org/10.1007/s11263-015-0816-y">10.1007/s11263-015-0816-y</a></li> </ul> <p>Open-access datasets that our machine learning workflow have been applied to:</p> <ul> <li>2022-AutoDetect-mNP-morphology.zip contains a selected TEM images of nanoparticles categorized in 3 morphologies from the AutoDetect-mNP datasets: DOI: <a href="http://doi.org/10.6078/D1WT44">10.6078/D1WT44</a> and DOI: <a href="http://doi.org/10.6078/D1S12H">10.6078/D1S12H</a></li> <li>2021-TEM virus.zip contains TEM images of 9 types of viruses from the TEM virus dataset. Matuszewski, Damian; Sintorn, Ida-Maria (2021), “TEM virus dataset”, Mendeley Data, V3, DOI: <a href="http://doi.org/10.17632/x4dwwfwtw3.3">10.17632/x4dwwfwtw3.3</a></li> </ul> <p>The official github page of the implementation of the machine learning models is <a href="https://github.com/arthijayaraman-lab/semi-supervised_learning_microscopy_images">semi-supervised_learning_microscopy_images</a>.</p> <p>If you use the dataset or the codes in the repository linked above, please cite the following <a href="https://doi.org/10.1039/D2DD00066K">manuscript</a>:</p> <p>S. Lu, B. Montz, T. Emrick and A. Jayaraman, <em>Digital Discovery</em>, 2022, <strong>1</strong>, 816-833 , <strong>DOI: </strong>10.1039/D2DD00066K</p>
Inverse design of viral infectivity-enhancing peptide fibrils from continuous protein-vector embeddings
<p>The Tables S3 - S5 are a supplement for the article "Inverse design of viral infectivity-enhancing peptide fibrils from continuous protein-vector embeddings" uploaded as a Preprint in ChemRxiv DOI: 10.26434/chemrxiv-2023-1kqm3</p>
Exploring Minor Proteins and Peptides in Human Milk: a Proteomic Analysis Across Lactation Stages
ClinicalTrials.gov study NCT06787963. IPD Sharing: NO. Countries: 1. Publications: 0.
Automated protein-protein structure prediction of the T cell receptor-peptide major histocompatibility complex
Open the record for dataset details and reuse information.
Epitope mapping of 5 monoclonal antibodies directed against meningococcal factor H binding protein by peptide microarray
GEO Series GSE98879. Homo sapiens; Neisseria meningitidis serogroup B. 5 samples. Type: Protein profiling by protein array.
Effect of Egg Protein Ovotransferrin-derived Peptide, IRW on Gene Expression of Vascular Tissues in Spontaneously Hypertensive Rats
GEO Series GSE65017. Rattus norvegicus. 11 samples. Type: Expression profiling by high throughput sequencing.
Ribosomal Proteins Regulate MHC Class I Peptide Generation for Immunosurveillance
GEO Series GSE114484. Homo sapiens. 14 samples. Type: Expression profiling by array.
ScienceDex guides
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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.