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72 results for “hairpin”
Molecular dynamics simulation data of designed β-hairpins
<p>Raw simulations data (protein only) and simulation set-up files of designed β-hairpins. More details can be found in this paper: </p> <p>Yunhui Ge, Brandon Kier, Niels H. Andersen and Vincent A. Voelz. <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.7b00132"><em>Computational and experimental evaluation of designed beta-cap hairpins using molecular simulations and kinetic network models.</em></a> J. Chem. Inf. Model., 2017, 57 (7), pp 1609–1620</p>
Replica exchange molecular dynamics simulation data of designed β-hairpins (implicit solvent, AMBER ff96)
<p>Raw REMD simulation data (protein only) of designed β-hairpins. AMBER ff96 and implicit solvent model is used. More details can be found in this paper: </p> <p>Yunhui Ge, Brandon Kier, Niels H. Andersen and Vincent A. Voelz. <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.7b00132"><em>Computational and experimental evaluation of designed beta-cap hairpins using molecular simulations and kinetic network models.</em></a> J. Chem. Inf. Model., 2017, 57 (7), pp 1609–1620</p>
Replica exchange molecular dynamics simulation data of designed β-hairpins (implicit solvent, AMBER ff99SB-ildn)
<p>Raw REMD simulation data (protein only) of designed β-hairpins. AMBER ff99SB-ildn and implicit solvent model is used. More details can be found in this paper: </p> <p>Yunhui Ge, Brandon Kier, Niels H. Andersen and Vincent A. Voelz. <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.7b00132"><em>Computational and experimental evaluation of designed beta-cap hairpins using molecular simulations and kinetic network models.</em></a> J. Chem. Inf. Model., 2017, 57 (7), pp 1609–1620</p>
Frustration Between Preferred States of Complementary Trinucleotide Repeat DNA Hairpins Anticorrelates with Expansion Disease Propensity
<p>The expansion of DNA trinucleotide repeats (TRs) beyond a threshold often results in neurodegenerative diseases in humans. The mechanisms causing these expansions remain unknown, although the tendency of TR ssDNA to self-associate into hairpins that slip along their length is widely presumed to be related. Here we apply single molecule FRET (smFRET) experiments and molecular dynamics simulations to determine conformational stabilities and slipping dynamics for CAG, CTG, GAC, and GTC hairpins. By developing novel analysis approaches for states with closely spaced FRET efficiencies along with improved transition detection algorithms, we determined the kinetic slipping schemes for these hairpins. Tetraloops are favored in CAG (89%), CTG (89%) and GTC (69%) while GAC favors triloops. We also determined that TTG interrupts near the loop in the CTG hairpin stabilize the hairpin against slipping (as do CAA substitutions in CAG hairpins). The different loop stabilities have implications for intermediate structures that may form when TR-containing duplex DNA opens. Opposing hairpins in the (CAG) ∙ (CTG) duplex would have matched stability whereas opposing hairpins in a (GAC) ∙ (GTC) duplex would have unmatched stability. This unmatched stability would introduce mechanical stress or frustration in the (GAC) ∙ (GTC) opposing hairpins that would be absent in (CAG) ∙ (CTG) structures. Given the biological observation that the CAG and CTG TR can undergo large, disease-related expansion whereas the GAC and GTC sequences do not, the mechanical stability differences we have identified can inform and constrain models of the expansion mechanisms of TR regions.</p>
Sequence-based identification of amyloidogenic β-hairpins
<p>Data for: Heid et al., Sequence-based identification of amyloidogenic β-hairpins reveals a prostatic acid phosphatase fragment promoting semen amyloid formation</p> <p> </p> <p>The dataset contains code and output sequences for sequence-based identification of amyloidogenic β-hairpins</p>
Frustration Between Preferred States of Complementary Trinucleotide Repeat DNA Hairpins Anticorrelates with Expansion Disease Propensity
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Hairpin protein partitioning from the ER to Lipid Droplets involves major structural rearrangements
<div> <p>The project includes dataset from MD simulations and EPR measurements.</p> <p>Description of the MD simulation dataset:<br>-Data type: MD simulations of UBXD8 peptide at varying depths/conformations in POPC bilayer, POPC/Triolein:Cholesteryl oleate monolayer, and in Bilayer-Lipid droplet setup. <br>-Force fields: All-atom simulations were carried out using Charmm36 force field. The parameters for Triolein and Cholesteryl oleate are derived from Olarte et al., 2020 and were obtained from the corresponding authors of that publication. Coarse-grained simulations were carried out using Martini force field. <br>-Simulation Package: All simulations were carried out using GROMACS 2021 simulation package.<br>-File types: The uploaded files include structure files in PDB format, input parameter files (.mdp), topology (topol.top), and force field files.</p> </div> <div>Description of the EPR dataset:<br>- Data type: Experimental spectroscopic measurements, Easyspin simulation and analysis<br>- Files are with filename extensions: DSC, DAT<br>- Information on origin of the data:<br>- EPR spectroscopic measurements with filename extensions DSC and DTA.<br>- EPR spectroscopic simulation and analyses with filename extension m.<br>- EPR simulations were generated using Easyspin version 5.2.36 and Matlab version 23.2.0.2428915.<br>- X-band CW-EPR spectroscopic measurements were generated by EMX spectrometer equipped with ER4123D cavity produced by Bruker.</div>
Force extension curves with hairpin
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Data set for "Structural transitions in the RNA 7SK 5' hairpin and their effect on HEXIM binding"
<p>Raw data set for "Structural transitions in the RNA 7SK 5' hairpin and their effect on HEXIM binding"</p> <p> </p> <p>Version 1.0: Energy landscape data and MD trajectories for RNA+ARM peptide</p>
The miRBase release 22 reference files: stem-loop sequences (hairpins) and mature miRNA sequences
<pre>The miRBase Sequence Database -- Release 22 ------------------------------------------- The miRBase database provides a searchable online repository for published microRNA sequences and associated annotation. miRBase also provides a gene naming and nomenclature function in the miRBase Registry. Release 22 of the database contains 38589 entries representing hairpin precursor miRNAs, expressing 48885 mature miRNA products, in 271 species. The data are freely available to all through the web interface at http://www.mirbase.org/ and in flatfile form from ftp://mirbase.org/pub/mirbase/. </pre>
Supplementary Data for "DNA hairpin base-flipping dynamics drives APOBEC3A recognition and selectivity"
<p>Contains CSV-formatted files with RMSD and Sugar Pucker averages and standard deviations for 3- and 4-nt hairpin loop simulations as described in the manuscript "DNA hairpin base-flipping dynamics drives APOBEC3A recognition and selectivity".</p>
Replica exchange molecular dynamics simulation data of designed β-hairpins (implicit solvent, AMBER ff99SB-ildn-nmr)
<p>Raw REMD simulation data (protein only) of designed β-hairpins. AMBER ff99SB-ildn-nmr and implicit solvent model is used. More details can be found in this paper: </p> <p>Yunhui Ge, Brandon Kier, Niels H. Andersen and Vincent A. Voelz. <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.7b00132"><em>Computational and experimental evaluation of designed beta-cap hairpins using molecular simulations and kinetic network models.</em></a> J. Chem. Inf. Model., 2017, 57 (7), pp 1609–1620</p>
A turn in species conservation for hairpin banksias: Demonstration of oversplitting leads to a better management of diversity
<p>We generated SNP genotype data and chloroplast genomic data to test the current taxonomy and infer a population-scale evolutionary scenario for the Hairpin Banksias (<em>B. collina, B. cunninghamii, B. neoanglica, B. spinulosa </em>and <em>B. vincentia</em>) and outgroups using a sample-set comprehensive in its representation of morphological diversity and a two-and-a-half thousand kilometer distribution. Here, we provide an archive of these SNP genotype and chloroplast sequence alignment data.</p>
FIGURE 1 in Analysis of primary structure loops from Hairpins 35 and 48 of the Nematoda SSU rRNA gene provides further evidence that the genera Tripylina Brzeski, 1963, Trischistoma Cobb, 1913 and Rhabdolaimus de Man, 1880 are members of Enoplida
FIGURE 1. Localisation of synapomorphic molecular traits in 18S r RNA genes of Enoplida. A. Fragments of alignments of aligned gene sequences corresponding to SSU rRNA regions of hairpins 35 and 48. Presumed synapomorphies of Trichistoma, Tripylina and other Enoplida are marked and given a dark background. B. Secondary structures of Hairpin 35 of Loricera foveata. C. Secondary structures of Hairpin 35 of Trischistoma and Tripylina. Arrowed, 1280 A → G substitution. D. Secondary structures of Hairpin 48 of Loricea foveata. E. Secondary structures of Hairpin 48 of Trischistoma and Tripylina. Arrowed: 1820 G → Y substitution.
A Putative New Role of Tv-PSP1 Recognizes IRE and ERE Hairpin Structures from Trichomonas vaginalis. Figure S1. Tv-PSP1 crystal packing. Figure S2. Tv-PSP1 secondary structure and general topology.
<p>Figure S1. Tv-PSP1 crystal packing. Crystal packing of the hexagonal space group P63 with cell dimensions<br> a=81.9 Å, b=81.9 Å, c=129.3 Å, and γ=120°. A) Trimer A in Grey surface is around the threefold axis symbol. B)<br> Trimer D in blue steel color, this trimer is under Trimer A on the same threefold axis. The trimer D on the final<br> structure is not visible in a large part of the structure, only are visible the fragments in contact with monomer A,<br> here was built a complete Trimer from previous refinement process to illustrate the position on the crystal.<br> C)Trimer B in green color is around the threefold axis symbol in the symmetric object of the twofold screw axis<br> of the cell. D)Trimer C in orange color is around the sixfold axis symbol. Figure was made in VMD program [39]. ID PDB: 7KGC.</p> <p> </p> <p>Figure S2. Tv-PSP1 secondary structure and general topology. A) Tv-PSP1 secondary structure of the<br> asymmetric unit monomers obtained with VMD program [39]. Marginal differences are observed on the L1 and<br> L7. B) General topology of the monomer A structure. Beta strands in yellow color, 3-10 helixes in blue color, alfa<br> helixes in magenta color, turns and coil in green color.</p>
Bone Hairpin, Roman, Cucufate, Portugal
Bone hairpin from roman villa of S. Cucufate, Alentejo, Portugal. High Roman Empire (1st century AD to 3rd century AD). This object of personal adornment was known in ancient Rome under the name of Acus crinalis. The piece has an stem of oval section, pointed at the end and almost spherical head. Its total length is 8.4 cm. Currently it is showcased in the permanent exhibition of the museum of S. Cucufate (Vila de Frades, Vidigueira). Catalog No. CUC. 79 XIV 7 (1). Processed and modeled in Reality Capture from 538 photos Source: Objaverse 1.0 / Sketchfab
A turn in species conservation for hairpin banksias: Demonstration of oversplitting leads to a better management of diversity
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MicroRNA Clustering Assists Processing of Suboptimal MicroRNA Hairpins Through the Action of the ERH Protein
GEO Series GSE142818. Homo sapiens. 4 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Engineering of a promoterless anti-viral RNAi hairpin into an endogenous miRNA locus
GEO Series GSE68638. Homo sapiens. 24 samples. Type: Non-coding RNA profiling by array; Expression profiling by array.
A 36-base hairpin within lncRNA DRAIC interacts with the IKKα coiled-coil domain, weakening the IKK complex and inhibiting NF-kappaB activation
GEO Series GSE279192. Homo sapiens. 2 samples. Type: Other.
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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.