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1,744 results for “peptide”
Molecular modeling of self-assembling peptides MELD structures
<p>Top 10 MELD structures for each system used in the "Molecular modeling of self-assembling peptides" paper.</p>
Dynamic interactome of the MHC I peptide loading complex in human dendritic cells - Source II
<p>Source data underlying MS data set (SFig.2). Datafile comprises MS raw files + MaxQuant output files.</p>
Dynamic interactome of the MHC I peptide loading complex in human dendritic cells - Source III
<p>Source data underlying Raji cell data set (SFig.3). Datafile comprises MS raw data + MaxQuant output files.</p>
Ultra-Accurate Correlation Between Precursor and Fragment Ions in Two-lDimensional Mass Spectrometry: Acetylated vs. Trimethylated Histone Peptides
<p>Two-dimensional mass spectrometry (2D MS) is a method<br> for tandem<br> mass spectrometry in which precursor and fragment ions are correlated<br> by manipulating ion radii rather than by ion isolation. A 2D mass<br> spectrum contains the fragmentation patterns of all analytes in a<br> sample, acquired in parallel. We report ultrahigh-resolution narrowband<br> 2D mass spectra of a mixture of two histone peptides with the same<br> sequence, one of which carries an acetylation and the other a trimethylation<br> (m/z 0.006 difference). We reduced<br> the distance between data points in the precursor ion dimension and<br> compared the accuracy of the precursor-fragment correlation with the<br> resolving power. We manage to perform label-free quantification on<br> the histone peptide mixture and show that precursor and fragment ions<br> can be accurately correlated even though the precursor ions are not<br> resolved. Finally, we show that increasing the resolution of a 2D<br> mass spectrum in the precursor ion dimension too far can lead to a<br> decline in the signal-to-noise ratio.</p>
Data from: Evolution of Large Aβ16-22 Aggregates at Atomic Details and Potential of Mean force Associated to Peptide Unbinding and Fragmentation Events
<p>This data accompanies the paper entitled <em>Evolution of Large Aβ16-22 Aggregates at Atomic Details and Potential of Mean force Associated to Peptide Unbinding and Fragmentation Events</em></p> <p>The zip archive contains the results of molecular dynamics simulations of the 2 systems investigated in the paper: the first one with 139 <em>Aβ16-22 </em><em>peptides, the second one with 106 peptides.</em><em> </em>Each system has been simulated at 300 K. Starting configurations of the peptides are provided for all the systems in GRO Gromos87 format. Trajectories with the positions of the peptides every 100 ps are provided for all the systems in XTC gromacs format. For system 1 we also provide XTC trajectories for all the replicas of the REST2 simulation.</p>
Comparative Study of Molecular Mechanics Force Fields for β-peptidic Foldamers: Folding and Self-Association
<p>Molecular dynamics simulation input files and Python scripts used for preparing the runs and analyzing the trajectories.</p>
Raw data for the article "Peptide-Hypervalent Iodine Reagent Chimeras: Enabling Peptide Functionalization and Macrocyclization"
<p>Raw NMR, HPLC and MS data for the article "Peptide-Hypervalent Iodine Reagent Chimeras: Enabling Peptide Functionalization and Macrocyclization" published in Angewandte Chemie, DOI: </p> <p><a href="https://doi.org/10.1002/anie.202306036">https://doi.org/10.1002/anie.202306036</a> </p> <p>The number of the folders either correspond to compounds numbers in the article or the name of the folder is self-describing. All details concerning conditions and equipment for measurements can be found in the supporting information of the article.</p>
Intrinsically Disordered Regions Promote Protein Refoldability and Facilitate Retrieval from Biomolecular Condensates–Peptide Quantifications
<p>Many eukaryotic proteins contain intrinsically disordered regions (IDRs) that intersperse globular folded domains, in contrast with bacterial proteins which are typically highly globular. Recent years have seen great progress in identifying biological functions associated with these elusive protein sequence: in specific cases, they mediate liquid- liquid phase separation, perform molecular recognition, or act as sensors to changes in the environment. Nevertheless, only a small number of IDRs have annotated functions despite their presence in 64% of yeast proteins, stimulating some to question what ‘general purpose’ they may serve. Here, by interrogating the refoldability of two fungal proteomes (Saccharomyces cerevisiae and Neurosporra crassa), we show that IDRs render their host proteins more refoldable from the denatured state, allowing them to cohere more closely to Anfinsen’s thermodynamic hypothesis. The data provide an exceptionally clear picture of which biophysical and topological characteristics enable refoldability. Moreover, we find that almost all yeast proteins that partition into stress granules during heat shock are refoldable, a finding that holds for other condensates such as P-bodies and the nucleolus. Finally, we find that the Hsp104 unfoldase is the principal actor in mediating disassembly of heat stress granules and that the efficiency with which condensed proteins are returned to the soluble phase is also well explained by refoldability. Hence, these studies establish spontaneous refoldability as an adaptive trait that endows proteins with the capacity to reform their native soluble structures following their extraction from condensates. Altogether, our results provide an intuitive model for the function of IDRs in many multidomain proteins and clarifies their relationship to the phenomenon of biomolecular condensation.</p> <p>This dataset provides peptide quantifications (and their respective P-values) from three separate types of experiments used to support the claims in this study.</p> <p>1. Peptide quantifications from global refolding reactions, assessed with limited-proteolysis mass spectrometry (LiP-MS), carried out on two fungal organisms (S. cerevisiae [yeast] & N. crassa), at three refolding times, repeated on three separate iterations (for yeast).</p> <p>2. Peptide quantifications from LiP-MS experiments conducted on yeast extracts during heat shock or recovery from heat shock</p> <p>3. Annotations for peptides in #1 that are associated with linker regions between folded domains.</p>
Antimicrobial peptides modulate lung injury by altering the intestinal microbiota
<p>This repository contains the OTU tables for "Antimicrobial peptides modulate pulmonary inflammation by altering the intestinal microbiota" by Abdelgawad and Nicola et al., an analysis of the role of antimicrobial peptide in the gut-lung axis during hyperoxia-induced lung injury. This work was supported by the National Heart, Lung, and Blood Institute of the U.S. National Institutes of Health, K NIH: K08 HL151907 (KW), K08 HL141652 (CL), K08 DK120871 (AO); the Kaul Pediatric Research Institute at Children’s of Alabama (KW), and the Microbiome Center at UAB (KW). The funding agencies had no role in the design, conduct, and analysis of the study or in the decision to submit the manuscript for publication. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. All data in this repository is the intellectual property of the authors and may be utilized for academic publication only with prior written permission.</p>
Amphiphilic Cyclic Antimicrobial Peptides Derived from the [W4R4] Scaffold: Structural Studies and Correlation with Activity
<p>Data for Publication “Amphiphilic Cyclic Antimicrobial Peptides Derived from the [W4R4] Scaffold: Structural Studies and Correlation with Activity.” The file archive "<em>WR_peptides_MD.zip</em>" contains the starting structures of peptides, molecular topologies of peptides, representative MD trajectories of peptides in water and the DOPC/DOPG bilayer, as well as MD simulation parameters. See the README.txt file in this archive for details.</p>
Supplementarty Data: Retention time and fragmentation predictors increase confidence in identification of common variant peptides
<p>Supplementary data related to the paper "Retention time and fragmentation predictors increase confidence in identification of common variant peptides"</p> <p>The database directory contains the FASTA files of the four protein sequence databases used in the analysis of the paper.</p> <p>The data directory contains exports with lists of all peptide-to-spectrum matches obtained from the analysis.</p> <p>More information and scripts to reproduce the post-processing steps are available at: https://github.com/ProGenNo/VariantPeptideIdentification</p>
Test-time training for deep MS/MS spectrum prediction improves peptide identification
<p>In bottom-up proteomics, peptide-spectrum matching is critical for peptide and protein identification. Recently, deep learning models have been used to predict tandem mass spectra of peptides, with the similarity scores of predicted and experimental spectra being integrated into peptide-spectrum matching. These models follow the supervised learning paradigm, which trains a general model using paired peptides and spectra from standard datasets and uses the model for prediction on experimental data. However, this approach can lead to inaccurate predictions due to differences between the training data and the experimental data, such as sample types, enzyme specificity, and instrument calibration. To address this issue, we proposed a Test-Time Training paradigm that adapts the pre-trained model to experimental data-specific models, namely PepT3. PepT3 results in a 10-40\% increase in peptide identification, depending on the distinctness of training and experimental data. Intriguingly, PepT3 improves the identification of tumor-specific neo-epitopes when applied to a complex patient-derived immunopeptidomic sample, with two-thirds of these neo-epitopes predicted to bind to the patient's human leukocyte antigen isoforms</p>
Data and code for: Somatostatin peptide signaling dampens cortical circuits and promotes exploratory behavior
<p>Our dataset reflects the data and code used in Brockway et al., Cell Reports. We sought to characterize the unique role of somatostatin (SST) in the prelimbic (PL) cortex. We perform slice electrophysiology in pyramidal and GABAergic neurons to characterize the pharmacological mechanism of SST signaling, and fiber photometry of GCaMP6f fluorescent calcium signals from SST neurons to characterize the activity profile of SST neurons during exploration of an elevated plus maze (EPM) and open field test (OFT). We used local delivery of a broad SST receptor (SSTR) agonist and antagonist to test causal effects of SST signaling. SSTR activation hyperpolarizes layer 2/3 pyramidal neurons, an effect that is recapitulated with optogenetic stimulation of SST neurons. SST neurons in PL are activated during EPM and OFT exploration, and SSTR agonist administration directly into the PL enhances open-arm exploration in the EPM. This work describes a broad ability for SST peptide signaling to modulate microcircuits within the prefrontal cortex and related exploratory behaviors.</p>
Simulation trajectories for CLas BamA protein interacting with high-affinity short peptides
<p>Trajectories of molecular dynamics simulations done using Schrodinger Desmond for interaction of BamA protein of <em>Candidatus </em>Liberibacter asiaticus with three short peptides with a high affinity towards BamA. Simulations were conducted for 100 ns. </p>
Computational Data Archive in Support of the Ping-Pong Mechanism for Peptide Bond Formation and Hydrolysis
<p>In search for the goldilocks zone in the chemical space for amino acid oligomerization that is relevant to the emergence of protein-based metabolism, we identified a significant gap in our understanding about how peptide bond is formed and hydrolyzed under ambient aqueous conditions. We identified a six-step mechanism that reproduces the experimentally known experimental barriers. By careful evaluation of a comprehensive set of levels of theory, modelling of solvation effect, and calculation of thermochemical parameters, we established a robust computational model to expand the bulk water focus to interfacial phenomena of atmospheric/hydrospheric and litospheric/hydrospheric boundaries. </p> <p>While we cannot travel back in time billions of years to witness the "birth" of the first macromolecule with pre-biotic relevance, we present the dataset and the corresponding publication in RSC Organic and Biomolecular Chemistry (July 26, 2023 issue) our attempt to establish an unbiased computational platform where we can evaluate experiments and generate experimentally testable ideas.</p>
Dataset for Peptide binder design with inverse folding and protein structure prediction
<p>Dataset for a paper on peptide design</p> <p> </p> <p><br> mutated_peptides - results for randomly intriduced mutations in protein-peptide complexes that can be predicted at 2 Å (Figure 1)<br> pdb_peptide - variation in the number of recycles (1-10) for 96 peptides (Figure 1)<br> minibinder - results for the minibinder set (Figure 2)<br> Pfam - results for the Pfam set (Figures 4+5)<br> protein_mpnn - results on protein_mpnn test set (Figure 6)</p> <p> </p> <p> </p>
Phase II Study of the Efficacy of Peptide T in HIV-Positive Individuals With Cognitive Impairment.
ClinicalTrials.gov study NCT00000392. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Folate Receptor Alpha Peptide Vaccine With GM-CSF Versus GM-CSF Alone in Patients With Platinum Sensitive Ovarian Cancer
ClinicalTrials.gov study NCT02978222. IPD Sharing: NO. Countries: 1. Publications: 1.
Racial Differences in the Natriuretic Peptide Response to Glucose Challenge
ClinicalTrials.gov study NCT03072602. IPD Sharing: NO. Countries: 1. Publications: 4.
Vaccine Therapy With Tumor Specific Mutated VHL Peptides in Adult Cancer Patients With Renal Cell Carcinoma
ClinicalTrials.gov study NCT00001703. IPD Sharing: Not stated. Countries: 1. Publications: 3.
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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.