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456 results for “motifs”
From poison to promotor –unique Rh4 structural motifs in supported rhodium sulphides as hydroformylation catalysts
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Motif enrichment analyses obtained by centriMo on human enhancers
<p>We applied Centrimo (Bailey and Machanick 2012) from the MEME suite version 4.11.1 with default parameters to DNA sequences of regions ± 500 bp around the mid-points of enhancers from class 1 (lower %GC) and class 2 (higher %GC). Class 1 enhancer regions were used as foreground and class 2 enhancer regions as background and vice-versa. The MEME databases of motifs<br> considered for enrichment were derived from (Jolma et al. 2013) (jolma2013.meme), JASPAR (Mathelier et al. 2015a) (JASPAR_CORE_2016_vertebrates.meme), Cis-BP (Weirauch et al. 2014) (Homo_sapiens.meme), Swiss Regulon (Pachkov et al. 2013) (Swiss_Regulon_human_and_mouse.meme), and HOCOMOCO (Kulakovskiy et al. 2016) (HOCOMOCOv10_HUMAN_mono_meme_format.meme). The same procedure was applied to promoter regions ( ± 500 bp around gene starts) associated with class 1 and class 2 enhancers.</p>
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study- Part 3
<p>Trajectories and input files for the simulations of the Rbfox·pre-miR20b complex.</p>
Molecular basis for the increased affinity of an RNA recognition motif protein engineered to re-direct its specificity -PART 5
<p>Trajectories and input files for the simulations (REST2, REST2-PS and unbiased MD) of the Rbfox*·pre-miR20b* complex.</p>
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study- PART 2
<p>Trajectories and input files of the simulations of the free pre-miR20b.</p>
Survival analysis of DNA mutation motifs with penalized proportional hazards
<p>Output used to produce the tables and figures in the manuscript:</p> <p>Feng and Shaw, et al. (2017) Survival analysis of DNA mutation motifs with penalized proportional hazards. <em>Annals of Applied Statistics</em>, <em>under revision</em>.</p> <p><br> Preprint: <a href="http://arxiv.org/abs/1711.04057">http://arxiv.org/abs/1711.04057</a></p> <p>Package: <a href="http://github.com/matsengrp/samm">http://github.com/matsengrp/samm</a></p> <p> </p> <p>See README.md for more information.</p>
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study-PART 7
<p>Simulations of the Rbfox*-miR20b and of the Rbfox-mir20b* complexes.</p>
[PART 3] A twist of fate: the helix-turn-helix motif in Pseudomonas aeruginosa ExsA can allosterically stabilize the ligand-binding domain
<p>1273- ExsA - Dimer1 without DNA - alphaFold compact - 230ns/day 10x500ns<br>*1274- ExsA - Dimer2 without DNA - xtal extended (like 1026) - 10x1µs (not everything is 1 µs)<br>1275- ExsA - Dimer3 without DNA - made by hand / 150ns/day (reps 1-5 broken, reps 6-10 correct)<br>*1276- ExsA- monomer - Site1-PexoT - 240 ns/day - 10x1µs (some replicas have pieces missing)<br>*1277- ExsA- monomer - Site2-PexoT - 10x1µs<br>*1278- ExsA - Dimer2 with broken DNA - xtal extended (like 1026) - 5x200ns?</p>
[PART 2] A twist of fate: the helix-turn-helix motif in Pseudomonas aeruginosa ExsA can allosterically stabilize the ligand-binding domain
<p>1273- ExsA - Dimer1 without DNA - alphaFold compact <br>1274- ExsA - Dimer2 without DNA - xtal extended <br>1275- ExsA - Dimer3 without DNA - made by hand (reps 1-5 broken, reps 6-10 correct)<br>1276- ExsA- monomer - Site1-PexoT <br>1277- ExsA- monomer - Site2-PexoT<br>1278- ExsA - Dimer2 with broken DNA</p>
Motif-guided Identification of KRAS-interacting Proteins
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Phytochemistry reflects different evolutionary history in traditional classes versus specialized structural motifs
<p>Foundational hypotheses addressing plant-insect codiversification and plant defense theory typically assume a macroevolutionary pattern whereby closely related plants have similar chemical profiles. However, numerous studies have documented variation in the degree of phytochemical trait lability, raising the possibility that phytochemical evolution is more nuanced than initially assumed. We utilize proton nuclear magnetic resonance (<sup>1</sup>H NMR) data, chemical classification, and double digest restriction-site associated DNA sequencing (ddRADseq) to resolve evolutionary relationships and characterize the evolution of secondary chemistry in the Neotropical plant clade Radula (<i>Piper</i>;<i> </i>Piperaceae). Sequencing data substantially improved phylogenetic resolution relative to past studies, and spectroscopic characterization revealed the presence of 35 metabolite classes. Metabolite classes displayed phylogenetic signal, whereas the crude <sup>1</sup>H NMR spectra featured little evidence of phylogenetic signal in multivariate tests of chemical resonances. Evolutionary correlations were detected in two pairs of compound classes (flavonoids with chalcones; <i>p</i>-alkenyl phenols with kavalactones), where the gain or loss of a class was dependent on the other's state. Overall, the evolution of secondary chemistry in Radula is characterized by strong phylogenetic signal of traditional compound classes and weak phylogenetic signal of specialized chemical motifs, consistent with both classic evolutionary hypotheses and recent examinations of phytochemical evolution in young lineages.</p>
Fragment screening using biolayer interferometry reveals ligands targeting the SHP-motif binding site of the AAA+ ATPase p97
<p>Biosensor techniques have become increasingly important for fragment-based drug discovery during the last years. The AAA+ ATPase p97 is an essential protein with key roles in protein homeostasis and a possible target for cancer chemotherapy. Currently available p97 inhibitors address its ATPase activity and globally impair p97-mediated processes. In contrast, inhibition of cofactor binding to the N-domain by a protein-protein-interaction inhibitor would enable the selective targeting of specific p97 functions. Here, we describe a biolayer interferometry-based fragment screen targeting the N-domain of p97 and demonstrate that a region known as SHP-motif binding site can be targeted with small molecules. Guided by molecular dynamics simulations, the binding sites of selected screening hits were postulated and experimentally validated using protein- and ligand-based NMR techniques, as well as X-ray crystallography, ultimately resulting in the first structure of a small molecule in complex with the N-domain of p97. The identified fragments provide insights into how this region could be targeted and present first chemical starting points for the development of a protein-protein interaction inhibitor preventing the binding of selected cofactors to p97.</p> <p><br> Here we publish the primary data of the biolayer-interferometry (BLI), STD-NMR, HSQC-NMR and mixed-solvent MD simulation results.<br> For BLI, the sensorgrams of 10 binding fragments identified in the screening are given. Measurements were conducted with the N-domain and the ND1-construct of p97. Additionaly, the measurements with ADP as positive control (n=6) are provided.<br> Four of the 10 fragments were selected as most promising hits for further investigation: TROLL2, TROLL7, TROLL8 and TROLL12. For these fragemnts, the STD-NMR build-up data, the HSQC-NMR spectra and the representative poses from the mixed solvent MD simulations used for CORCEMA predictions are provided. For TROLL2 the anomalous map of the bromine atom of the crystal structure (PDB entry: 7PUX) is given.</p>
Titration of poly-T amphiphile-motifs
<p>Microscopy data of DNA-nanomotifs (color channel 1) and amphiphile-nanomotifs (color channel 2). DNA-nanomotifs were mixed with a different ratio of control- and amphiphile-motifs in 20%-steps. Imaging was performed at an ambient temperature of 40°C inside the microscope enclosure. The repository contains miscroscope software data (NIS elements) as well as the scripts used for segmentation of DNA-droplets and analysis.</p> <p>Additional image information</p> <p>Objective: Apo LWD 40x WI λS DIC N2</p> <p>Width: 232.375 microns (1430)<br> Height: 168.35 microns (1036)<br> Depth: 12.6 microns (21)<br> Size: 119MB<br> Resolution: 6.1538 pixels per micron<br> Voxel size: 0.1625x0.1625x0.6 micron^3</p>
Fig. 4 in Meroterpenoids containing benzopyran or benzofuran motif from Ganoderma cochlear
Fig. 4. Comparison of the calculated ECD and experimental CD spectra in MeOH. A: The calculated ECD spectrum of (1R,2S,3R)-1 at CAM-B3LYP/ def2SVP level, σ = 0.20 eV; shift = 0 nm. B: The calculated ECD spectrum of (3S)-2 at CAM-B3LYP/def2SVP level, σ = 0.2 eV; shift = +23 nm.
Fig. 6. NRK-52 E in Meroterpenoids containing benzopyran or benzofuran motif from Ganoderma cochlear
Fig. 6. NRK-52 E cells were incubated with TGF-β1 (10 ng/mL) for 48 h in the absence or presence of substances (20 μM). Antibodies are fibronecitn, collagen I, α-SMA. GW was used as a positive control. GW: GW788388.
Fig. 5 in Meroterpenoids containing benzopyran or benzofuran motif from Ganoderma cochlear
Fig. 5. Meroterpenoids attenuate PA-induced IR in myotubes. (A) C2C12 cell proliferation in response to substances at 20 μM by CCK-8 assay. (B) Substances improved insulin-stimulated glucose uptake in IR model. (C–D) C2C12 were treated with substances at 20 μM for 24 h in IR model, and the expression of p-AKT was determined by using Western blot analysis. Substances ()-1, (+)-2 and (+)-9 improved insulin-stimulated glucose uptake in a dose-dependent manner. Metformin (Met) was used as a positive control. ##P <0.01 compared with no-PA treatment control; *P <0.05 and **P <0.01 compared with insulin treatment alone.
Characterization of signal and transit peptides based on motif composition and taxon-specific patterns
<p>These files contain data, sequences and supplementary information for the article entitled '<em>Characterization of signal and transit peptides based on motif composition and taxon-specific patterns</em>'.</p> <p><strong>Contents</strong></p> <ol> <li><strong>Raw_data.zip</strong> - contains raw data and sequences downloaded from UniProt and other databases. These files were used to create datasets used for described analyses.</li> <li><strong>Datasets.zip</strong> - presequence and peptide datasets obtained from raw data and used for all subsequent analyses.</li> <li><strong>Motif_analysis_reports_presequences_AMP.zip</strong> - HTML reports with detailed analyses of motif composition of presequences and AMPs</li> <li><strong>Motif_analysis_reports_presequences_encoded.zip</strong> - HTML reports with detailed analyses of motif composition of presequences using reduced alphabets</li> <li><strong>Motif_analysis_reports_presequences_taxonomy.zip</strong> - HTML reports with detailed analyses of motif composition of presequences for different taxons</li> <li><strong>Motif_analysis_reports_SP_taxonomy.zip</strong> - HTML reports with detailed analyses of motif composition of signal peptides on different taxonomic levels</li> <li><strong>Motif_analysis_reports_presequences_counts.zip </strong> - HTML reports with detailed analyses of motifs occuring more than once in presequences and AMPs</li> </ol> <p> </p> <p><strong>Abstract</strong></p> <p>Targeting peptides or presequences are N-terminal extensions of proteins that encode information about their cellular localization. They include signal peptides (SP), which target proteins to the endoplasmic reticulum (ER), and transit peptides (TP) directing proteins to the organelles of endosymbiotic origin: chloroplasts and mitochondria. TPs were hypothesized to have evolved from antimicrobial peptides (AMPs), which are responsible for the host defence against microorganisms, including bacteria, fungi and viruses. In this study, we performed a comprehensive bioinformatic analyses of amino acid motifs of targeting peptides and AMPs using a curated set of experimentally verified proteins. We identified motifs frequently occurring in each type of presequence showing specific patterns associated with their amino acid composition, and investigated their position within the presequence. We also compared motif patterns among different taxonomic groups and identified taxon-specific features, providing some evolutionary insights. Considering the functional relevance and many practical applications of targeting peptides and AMPs, we believe that our analyses will prove useful for their design, and better understanding of protein import mechanism and presequence evolution.</p>
Fig. 5. SSR motifs distribution. The X in Transcriptome sequencing of the apricot (Prunus armeniaca L.) and identification of differentially expressed genes involved in drought stress
Fig. 5. SSR motifs distribution. The X-axis is SSR type, the Y-axis value is the coordinate, the specific number of repetitions should correspond to the legend according to the color, and the Z-axis is the number of SSR. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Dataset associated with the study titled "Systematic discovery of regulatory motifs associated with human insulator sites" It includes data used for predicting insulator-associated DNA-binding proteins.
<p><strong>This dataset was used in the study on the prediction of insulator-associated DNA-binding proteins.</strong></p> <p>The three files included here are intended for use with the code available in the following GitHub repository:<br><a href="https://github.com/reposit2/insulator" target="_new" rel="noopener">https://github.com/reposit2/insulator</a></p> <p>To use the data, extract all three files and place them in the same directory as the code files.</p>
Homotypic motifs from 5 databases in the promoters of 21 plant species
<p><strong>What is this about:</strong></p> <p>This project encompasses multiple plant species, primarily employing tools like FIMO and PMET index to search for homotypic motifs in the promoters across various plant species. We selected five different sources of motifs: <strong>CIS-BP2</strong>, <strong>Franco-Zorrilla et al. 2014</strong>, <strong>Jaspar plants non redundant 2022</strong>, <strong>PlantTFDB</strong> and <strong>Plant Cistrome DB</strong>.</p> <p>Our research delves into an extensive analysis of gene expression regulatory elements, aiming to unravel the mechanisms of plant gene expression regulation. For this purpose, we have pre-calculated a vast amount of data in order to identify promoter patterns that consistently appear across different species. These promoter patterns potentially play fundamental and crucial regulatory roles in each species.</p> <p><strong>How to use it:</strong></p> <p>All data are prepared for PMET-Shiny app: <a href="https://github.com/duocang/PMET-Shiny-App">https://github.com/duocang/PMET-Shiny-App</a>.</p> <p>After downloading, all files are unzipped and put in the folder of <em><strong>data/indexing</strong></em> of PMET-Shiny.</p>
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.