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1,805 results for “molecule”
Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing
<p>Genes in prokaryotic genomes are often arranged into clusters and co-transcribed into poly- cistronic RNAs. Isolated examples of polycistronic RNAs were also reported in some higher eukaryotes but their presence was generally considered rare. Here we developed a long- read sequencing strategy to identify polycistronic transcripts in several mushroom forming fungal species including Plicaturopsis crispa, Phanerochaete chrysosporium, Trametes ver- sicolor, and Gloeophyllum trabeum. We found genome-wide prevalence of polycistronic transcription in these Agaricomycetes, involving up to 8% of the transcribed genes. Unlike polycistronic mRNAs in prokaryotes, these co-transcribed genes are also independently transcribed. We show that polycistronic transcription may interfere with expression of the downstream tandem gene. Further comparative genomic analysis indicates that polycis- tronic transcription is conserved among a wide range of mushroom forming fungi. In sum- mary, our study revealed, for the first time, the genome prevalence of polycistronic transcription in a phylogenetic range of higher fungi. Furthermore, we systematically show that our long-read sequencing approach and combined bioinformatics pipeline is a generic powerful tool for precise characterization of complex transcriptomes that enables identifica- tion of mRNA isoforms not recovered via short-read assembly.</p>
A machine learning-based high-precision density functional method for drug-like molecules
<h2><strong>Models</strong></h2><p>The repo contains the models and test datasets for our aticles. The energy unit is in <strong>Hartree,</strong> The coordinate unit is in<strong> Bohr.</strong></p><p><strong>## DeePHF</strong></p><p>you need first prepare the `dm_eig.npy` in data_test and do predict `l_e_delta.npy`, you can use</p><p>```</p><p>deepks test -m model.pth -o test/test -d data_test/* -D dm_eig -G</p><p>```</p><p><strong>## DeePKS</strong></p><p>first you should prepare the `atom.npy`, and `energy.npy` in data_test. you can test the datasets by command. </p><p>```</p><p>deepks scf scf_input.yaml -m model.pth -s data_test -d test_out</p><p>```</p><p><strong># Datasets</strong></p><p>All datasets only have `atom.npy` and `energy.npy`. The coordinate unit is `bohr`, and energy unit is `Hartree`.</p><p><strong>## small molecules torsion</strong></p><p>Contains 62 small molecules with 36 conformation for each under CCSD(T)/def2-TZVP.</p><p><br> </p><p>[1] B. D. Sellers, N. C. James, A. Gobbi, A comparison of quantum and molecular mechanical methods to estimate strain energy in druglike fragments, Journal of chemical information and modeling 57 (6) (2017) 1265–127</p><p><br> </p><p><strong>## MPCONF91</strong></p><p>Contains 6 molecules with 91 conformations under LNO-CCSD(T)/def2-TZVP.</p><p><br> </p><p>[1] J. Rezac, D. Bím, O. Gutten, L. Rulisek, Toward accurate conformational energies of smaller peptides and medium-sized macrocycles: Mpconf196 benchmark energy data set, Journal of chemical theory and computation 14 (3) (2018) 1254–1</p><p><br> </p><p><strong>## torsionNet206</strong></p><p>Contains 206 molecules with 4494 conformations under CCSD(T)/def2-TZVP.</p><p><br> </p><p>[1] B. K. Rai, V. Sresht, Q. Yang, R. Unwalla, M. Tu, A. M. Mathiowetz,G. A. Bakken, Torsionnet: A deep neural network to rapidly predict small-molecule torsional energy profiles with the accuracy of quantum mechanics, Journal of Chemical Information and Modeling 62 (4) (2022) 785–80</p><p><br> </p><p><strong>## Out-of-plane bending</strong></p><p>Contains 242 molecules with 3315 conformations under CCSD(T)/def2-TZVP.</p><p><br> </p><p>[1] X. Yang, C. Liu, P. Ren, High order ab initio valence force field with chemical pattern based parameter assignment., Journal of Computational Biophysics and Chemistry 21 (4) (2021) 43</p><p><br><br> </p><p><strong>## DrugBank-T</strong></p><p>Contains 165 molecules with 1155 conformations under CCSD(T)/def2-TZVP.</p><p><br> </p><p>[1] V. Law, C. Knox, Y. Djoumbou, T. Jewison, A. C. Guo, Y. Liu, A. Maciejewski, D. Arndt, M. Wilson, V. Neveu, et al., Drugbank</p><p>4.0: shedding new light on drug metabolism, Nucleic acids research 42 (D1) (2014) D1091–D1097 </p><p>[2] Z. Qiao, M. Welborn, A. Anandkumar, F. R. Manby, T. F. Miller III, Orbnet: Deep learning for quantum chemistry using symmetry adapted atomic-orbital features, The Journal of chemical physics 153 (12) (2020) 124111</p><p><strong>## Notice</strong></p><p>if you use above datasets, please cite the original articals too</p>
Data and code for "Tweezepy: A Python package for calibrating forces in single-molecule video-tracking instruments"
<p>Data and code for "Tweezepy: A Python package for calibrating forces in single-molecule video-tracking instruments."</p> <p>Data includes representative real and simulated bead trajectories used in the manuscript.</p> <p>Code includes all simulations, analysis, and plot details for the Figures in the manuscript. </p> <p>See included README.txt for more details.</p>
Docking of GSH and BPG to the hemoglobin molecule in the oxy and deoxy state
<p>Oxy-Hb contains four bound GSH molecules inside the cavity, two of them at the β-β interface (sites 1 and 2) and two at the α-α chains interface (sites 3 and 4). In deoxy-Hb, two GSH molecules from the β-β subunits interface are released from the sites 1 and 2 allowing BPG to bind. Reoxygenation of Hbb is associated with release of BPG from its binding site and binding of two GSH molecules to the sites 1 and 2. The sites 3 and 4 remain occupied by GSH independent of the Hb conformation.</p>
CH3CH2OCH3 molecule 200 ps MD trajectory with energies and forces
<p>Forces and Energies for 200 ps MD trajectory of OCH2C2H6 molecule by xTB/GFN-2, NVE ensemble</p> <p>--------------------------------------------------</p> <p>MD params:</p> <p>temp = 300.0 K / 500.0 K<br> time = 200.0 ps<br> dump time = 10.0 fs<br> step = 0.4 fs</p> <p> </p> <p>SOAP params:</p> <p>species=["H", "C", "O"],</p> <p>periodic=False,</p> <p>rcut=5.0,</p> <p>sigma=0.5,</p> <p>nmax=5,</p> <p>lmax=5,</p> <p>average="outer" / "inner",</p> <p>crossover=True,</p> <p>dtype="float64",</p> <p>------------------------------------------------</p> <p>SOAP invariants were calculated with DScribe library (https://pypi.org/project/dscribe/1.2.1/)</p> <p> </p> <p>Energies and forces are in eV and eV/Angstrom</p> <p>Filenames are intended to be self-explanatory</p> <p>Dataset is intended to be used for machine learning algorithms tests.</p>
Data of publication 'Optical spin-state polarization in a binuclear europium complex towards molecule-based coherent light-spin interfaces'
<p>Data of publication 'Optical spin-state polarization in a binuclear europium complex towards molecule-based coherent light-spin interfaces' by Kuppusamy Senthil Kumar et al. The two versions of Fig. 4d datasets correspond to the preprint version (https://zenodo.org/record/4905692#.Ymj9odpBxaQ) and publication version (https://www.nature.com/articles/s41467-021-22383-x), since a new set of data was taken during the review process. </p>
Single molecule videos related to "MCM complexes are barriers that restrict cohesin-mediated loop extrusion" Part 2/3
<p>Videos of cohesin translocation and collisions between translocating cohesin and MCMs under physiological salt conditions collected with MicroManager 1.4 as tif image sequences. Vidoes of DNA stained with SYTOX Orange after collection of cohesin translocation are included as separate image sequences.</p>
Single molecule videos related to "MCM complexes are barriers that restrict cohesin-mediated loop extrusion" Part 1/3
<p>Videos of collisions between translocating cohesin and MCMs under high salt conditions collected with MicroManager 1.4 as tif image sequences. Vidoes of DNA stained with SYTOX Orange after collection of cohesin translocation are included as separate image sequences.</p>
Single molecule videos related to "MCM complexes are barriers that restrict cohesin-mediated loop extrusion" Part 3/3
<p>Videos of collisions between translocating cohesin and MCM containing the YDF motif under physiological salt conditions collected with MicroManager 1.4 as tif image sequences. Videos of DNA stained with SYTOX Orange after collection of cohesin translocation are included as separate image sequences.</p>
Molecule dataset used in workflow memoization experiments
<p>This is a collection of Simplified Molecular Input Line Entry System (SMILES) strings that we used to evaluate our workflow memoization system in:</p> <p>> Vassiliadis, V., Johnston, A. M., McDonagh, L. J. "Fast, Transparent, and High-Fidelity Memoization Cache-Keys for Computational Workflows." 2022 IEEE International Conference on Services Computing (SCC). IEEE, 2022.</p>
Dynamic FRET example videos related to "Mars, a molecule archive suite for reproducible analysis and reporting of single-molecule properties from bioimages"
<p>Videos of dynamic switching between iso-I and iso-II conformations of a holiday junction at 50 mM Magnesium resulting in high and low FRET from Cy3 and Alexa647 labels positioned on the arms. Holiday junctions are surface immobilized through a biotin attachment and imaged using TIRF microscopy. The camera sensor is split using a dual view so that the acceptor emission is on the top and the donor emission is on the bottom. Videos from each position are provided as compressed zip files containing a sequence of tif files and associated metadata text file. Image sequences were collected using Micro-Manager 2.0 using ALEX or alternating laser excitation with alternating 637 and 532 pulses separated as two different channels. Beam profile images are provided for 637 and 532 excitation allowing for correction of the non-uniform beam profiles. The following 2D affine transformation matrix can be used to transform from the top acceptor emission region to the bottom donor emission region during processing.</p> <p>Affine 2D transformation from top to bottom: (m00, m01, m02, m10, m11, m12), (1.00276, 0.000208, 1.01236, 0.000267, 1.00312, 507.21025)</p> <p>A detailed image processing workflow for this dataset using Mars can be found under the example section at <a href="https://duderstadt-lab.github.io/mars-docs/">https://duderstadt-lab.github.io/mars-docs/</a> or directly at <a href="https://duderstadt-lab.github.io/mars-docs/examples/FRET_dynamic/">https://duderstadt-lab.github.io/mars-docs/examples/FRET_dynamic/</a></p>
XTB2-MolData : Dataset of 12 Million Molecules
<p>This dataset is an open chemistry database containing optimized molecular geometries and electronic properties calculated by the GFN2-xTB method (<a href="https://doi.org/10.1002/wcms.1493">C. Bannwarth et al.</a>) for 12.6 million organic molecules contained C, H, O, and N atoms.</p> <p>The initial geometries, before optimization by GFN2-xTB method, are taken from PubChem PM6 (<a href="https://doi.org/10.1021/acs.jcim.0c00740">Shimazaki et al.</a>) database.</p> <p>We also include our python code to manage a large molecule database. This code includes scripts to generate input files for Gaussian software, to read Gaussian output files, to create a small reduced dataset based on clustering algorithm, and many scripts to analyze the molecular properties included in the database.</p> <p>This code can be also taken from github: <a href="https://github.com/Castaneche/MolDataFW">https://github.com/Castaneche/MolDataFW</a>.</p>
Supporting Information for Disclosing Spin-Polarized Bonds on Isolable Molecules
<p>The file corresponds to the Bachelor Thesis of Ms. Elena Paulus. It contains the xyz coordinates of all optimized structures and their corresponding electronic energy in Hartree.</p>
Single molecule dataset for article: Multistep orthophosphate release tunes actomyosin energy transduction
<table> <tbody> <tr> <td> <p>Dataset (single molecule movies) that is behind the results in the article's Figure 2 and Figure 3.</p> <p>MATLAB scripts used to analyze the dataset. </p> </td> </tr> </tbody> </table> <p> </p>
Data for "Hot-carrier transfer across a nanoparticle-molecule junction: The importance of orbital hybridization and level alignment"
<p>This upload includes the data presented and analyzed in the article "Hot-carrier transfer across a nanoparticle-molecule junction: The importance of orbital hybridization and level alignment" by Jakub Fojt, Tuomas P. Rossi, Mikael Kuisma, and Paul Erhart.</p> <p>The codes for reproducing the data are provided at <a href="https://doi.org/10.5281/zenodo.7118376">doi:10.5281/zenodo.7118376</a>.</p> <p>See <em>README.md</em> in <em>data.zip</em> for a detailed description.</p>
Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α-Fig. 2def
<p>smTIRF-FRET Data for Fig 2, for "Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α"</p>
Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α-Fig. 7cde
<p>smTIRF-FRET Data for Fig 7, for "Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α"</p>
Apples to Apples: Shift from Mass Ratio to Additive Molecules per Electrode Area to Optimize Li-Ion Batteries
<p>Electrolyte additives in liquid electrolyte batteries can trigger the formation of a protective interphase (SEI) atthe electrodes that aims to suppress side reactions at the electrodes. Studies of varying amounts of additives have been done over the last years, providing a comprehensive understanding of the impact of the electrolyte formulation on the lifetime of the cells. However, these studies mostly focus on the variation of the mass fraction of additive in the electrolyte while disregarding the ratio (radd) of the additive's amount of substance (nadd) to the electrode area (Aelectrode). Herein we utilize our extremely accurate automatic battery assembly system (AUTOBASS) to vary electrode area and amount of substance of the additive. The data provides strong evidence that reporting the mass ratios of electrolyte components is insufficient and the mol of additive relative to the electrodes' area should be reported. Herein, the two most utilized additives, namely fluoroethylene carbonate (FEC) and vinylene carbonate (VC) were studied. Each additive was varied from 0.1 wt.-% - 3.0 wt.-% for VC, and 5 wt.-% - 15 wt.-% for FEC for two mass loadings of 1 mAh/cm2 and 3 mAh/cm2. To engage the community to find better descriptors, such as the proposed radd, we publish the dataset alongside this manuscript.</p> <p>Codes and mechanical parts of the project:</p> <p>AutoBASS 2.0: <a href="https://github.com/Helge-Stein-Group/AutoBASS/tree/AutoBASS_2.0">GitHub - Helge-Stein-Group/AutoBASS at AutoBASS_2.0</a></p>
Data for "Vertical characterization of highly oxygenated molecules (HOMs) below and above a boreal forest canopy"
<p>This excel file consists of the data been analyzed in the manuscript "Vertical characterization of highly oxygenated molecules (HOMs) below and above a boreal forest canopy". For more details, please contact the author (qiaozhi.zha@helsinki.fi). </p>
Data and code for "Strong plasmon-molecule coupling at the nanoscale revealed by first-principles modeling"
<p>The data includes atomic structures, time-dependent dipole moments, and photoabsorption spectra of the systems modeled and analyzed in the article "Strong plasmon-molecule coupling at the nanoscale revealed by first-principles modeling" by Tuomas P. Rossi, Timur Shegai, Paul Erhart, and Tomasz J. Antosiewicz.</p> <p>The input scripts for reproducing the data are also included. The time-dependent density-functional theory calculations use the LCAOTDDFT module of <a href="https://wiki.fysik.dtu.dk/gpaw/">the GPAW code</a>, and the atomic structures are created with <a href="https://wiki.fysik.dtu.dk/ase/">the ASE code</a>.</p> <p>See <em>README.md</em> in the archive for a detailed description.</p>
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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.