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773 results for “bounds”
Molcular Dynamics Trajectories for Delta Opioid Receptor bound with C6-Quino
<p>Molecular Dynamics Data for publication at Nature Communications, doi.org/10.1038/s41467-025-57734-5.</p> <p>Balazs R. Varga1#, Sarah M. Bernhard1#, Amal El Daibani1#, Saheem Zaidi2#, Jordy H. Lam2, Jhoan Aguilar1, Kevin Appourchaux1, Antonina Nazarova2, Alexa Kouvelis1, Ryosuke Shinouchi3, Haylee R. Hammond3, Shainnel O. Eans3, Violetta Weinreb4, Elyssa B. Margolis5, Jonathan F. Fay6, Xi-Ping Huang4, Amynah Pradhan1, Vsevolod Katritch2*, Jay P. McLaughlin3*, Susruta Majumdar1* and Tao Che1*</p> <p>Structure-guided design of partial agonists at an opioid receptor</p> <p>This folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.5 ns per frame. Periodic boundary condition (pbc) can be restored using VMD's standard pbc commands.</p> <p>Please cite us if you find this data useful!</p>
Molcular Dynamics Trajectories for Delta Opioid Receptor bound with C5-Quino
<p>Molecular Dynamics Data for publication at Nature Communications, doi.org/10.1038/s41467-025-57734-5.</p> <p>Balazs R. Varga1#, Sarah M. Bernhard1#, Amal El Daibani1#, Saheem Zaidi2#, Jordy H. Lam2, Jhoan Aguilar1, Kevin Appourchaux1, Antonina Nazarova2, Alexa Kouvelis1, Ryosuke Shinouchi3, Haylee R. Hammond3, Shainnel O. Eans3, Violetta Weinreb4, Elyssa B. Margolis5, Jonathan F. Fay6, Xi-Ping Huang4, Amynah Pradhan1, Vsevolod Katritch2*, Jay P. McLaughlin3*, Susruta Majumdar1* and Tao Che1*</p> <p>Structure-guided design of partial agonists at an opioid receptor</p> <p>This folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.5 ns per frame. Periodic boundary condition (pbc) can be restored using VMD's standard pbc commands.</p> <p>Please cite us if you find this data useful!</p>
Schrödinger's Red Pixel by Quasi Bound-States-In-the-Continuum
<p>The uploaded dataset contains the raw data and codes for the paper to be published on Science Advances, with the manuscript title of "Schrödinger’s Red Pixel by Quasi Bound-States-In-the-Continuum".</p>
Supplementary Movies: "Probing the dynamics of Streptococcus pyogenes Cas9 endonuclease bound to sgRNA complex using hydrogen-deuterium exchange mass spectrometry"
<p>Movies related to the article "Probing the dynamics of Streptococcus pyogenes Cas9 endonuclease bound to sgRNA complex using hydrogen-deuterium exchange mass spectrometry" in the International Journal of Molecular Science. "MD_Movie_Cas9_sgRNA_DNA" is the video of SpCas9-sgRNA-DNA complex behavior during 50 ns molecular dynamics simulation. In this movie, SpCas9 protein domains are shown in the following colors: REC lobe (green), CTD (blue), RuvC (pink), L-I-II (yellow), Arg (violet), and HNH (orange). RNA presented in cyan, and DNA -in dark blue.</p> <p>Movies "SpCas9_HeatMap" and "SpCas9-sgRNA_HeatMap" show the hydrogen exchange levels superimposed onto the protein structure obtained from MD trajectories. Relative uptake level presented at the time points of 10 s, 30 s, 1 min, 2 min, 5 min, 10 min, 30 min, 60 min, 120 min, 240 min, 360 min, and 480 min. The exchange scale is shown in a rainbow color scheme, where blue corresponds to the minimum uptake, while red corresponds to the highest observed uptake.</p>
Dataset (II) related to publication: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist
<p>MD simulation data related to the publication Rashidian et al.: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist. <a href="https://doi.org/10.1016/j.csbj.2022.06.020">https://doi.org/10.1016/j.csbj.2022.06.020</a></p> <p>Individual .zip files contain raw-desmond trajectories (-out.cms files and trj-files)</p> <p>dataset I: systems SRL+Co, C-100 and BAY-1797</p> <p>dataset I: each file contains all branched replicas and the main replica.</p> <p>dataset1: C_100_Replica1 contains four branched replicas and the main replica. The two of four branched replicas which stem from the middle of the main replica named: b_c_D1_r1_2285 (corresponding name in the SI data is R1_a) and b_c_D1_2285_r1_2 (corresponding name in the SI data is R1_b).</p> <p>dataset1: C_100_Replica2–5 , each file contains one main replica and the two branches.</p> <p>dataset I: system SRL+Co ;each file contains one main replica</p> <p>dataset I: system BAY-1797; each file contains one main replica</p> <p>dataset II:system SRL ; each file contains one main replica.</p>
Dataset (I) related to publication: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist
<p>MD simulation data related to the publication Rashidian et al.: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist. <a href="https://doi.org/10.1016/j.csbj.2022.06.020">https://doi.org/10.1016/j.csbj.2022.06.020</a></p> <p>Individual .zip files contain raw-desmond trajectories (-out.cms files and trj-files)</p> <p>dataset I: systems SRL+Co, C-100 and BAY-1797</p> <p>dataset I: each file contains all branched replicas and the main replica.</p> <p>dataset1: C_100_Replica1 contains four branched replicas and the main replica. The two of four branched replicas which stem from the middle of the main replica named: b_c_D1_r1_2285 (corresponding name in the SI data is R1_a) and b_c_D1_2285_r1_2 (corresponding name in the SI data is R1_b).</p> <p>dataset1: C_100_Replica2–5 , each file contains one main replica and the two branches.</p> <p>dataset I: system SRL+Co ;each file contains one main replica</p> <p>dataset I: system BAY-1797; each file contains one main replica</p> <p>dataset II:system SRL ; each file contains one main replica.</p>
Substrate recognition and cryo-EM structure of the ribosome-bound TAC toxin of Mycobacterium tuberculosis
<p>Datasets for the Figures 2 and S2 of the manuscript "Substrate recognition and cryo-EM structure of the ribosome-bound TAC toxin of Mycobacterium tuberculosis".</p> <p> </p> <p>The HTML files describe the analysis and the raw counts after nEMOTE-conv treatment.</p> <p>There are 5 files for each MMEMOTExx dataset:</p> <p>EmoteBarcodesReport.csv = summary<br> UnambNegTable.csv = counts of unique cuts on the reverse strand<br> UnambPosTable.csv = counts of unique cuts on the forward strand<br> AmbPosTable.csv = counts of all cuts on the forward strand<br> AmbNegTable.csv = counts of all cuts on the reverse strand</p> <p> </p>
ProtNAff: Protein-bound Nucleic Acid filters and fragment libraries
<p>This dataset contains the library produced by the ProtNAff tool for the paper.</p> <p>The files are in the numpy format matrix.</p> <p>There are files for the reduced and the all atoms fragments.</p>
Dataset (III) related to publication: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist
<p>MD simulation data related to the publication Rashidian et al.: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist. <a href="https://doi.org/10.1016/j.csbj.2022.06.020">https://doi.org/10.1016/j.csbj.2022.06.020</a></p> <p>Individual .zip files contain raw-desmond trajectories (-out.cms files and trj-files)</p> <p>dataset I: systems SRL+Co, C-100 and BAY-1797</p> <p>dataset I: each file contains all branched replicas and the main replica.</p> <p>dataset1: C_100_Replica1 contains four branched replicas and the main replica. The two of four branched replicas which stem from the middle of the main replica named: b_c_D1_r1_2285 (corresponding name in the SI data is R1_a) and b_c_D1_2285_r1_2 (corresponding name in the SI data is R1_b).</p> <p>dataset1: C_100_Replica2–5 , each file contains one main replica and the two branches.</p> <p>dataset I: system SRL+Co ;each file contains one main replica</p> <p>dataset I: system BAY-1797; each file contains one main replica</p> <p>dataset II:system SRL ; each file contains one main replica.</p> <p>dataset III:system C-100+Co (compound 100 in presence of SRC-1 coactivator) ; each file contains one main replica.</p>
Data for "Workhorse minimally-empirical dispersion-corrected density functional, with tests for weakly-bound systems: r2 SCAN + rVV10"
<p>VASP inputs and outputs for the:</p> <ul> <li>Ar2 binding energy curve (Ar2_bpara.tar.gz)</li> <li>L28 set of layered-solid geometries and interlayer binding energies (L28.tar.gz)</li> <li>S22 set of interaction energies of weakly-bound complexes (S22.tar.gz)</li> </ul> <p>All POTCAR files have been replaced by "potcar.txt" files containing the title(s) of the POTCAR(s) needed to reproduce the calculations. A preprint is available from the arXiv:2204.11717 (<a href="https://arxiv.org/abs/2204.11717">link</a>).</p>
Laboratory Assessment of the Impact of Chemical Oxidation, Mineral Dissolution, and Heating on the Nitrogen Isotopic Composition of Fossil-bound Organic Matter
<p>Results of laboratory experiments reported in the manuscript "<em>Laboratory Assessment of the Impact of Chemical Oxidation, Mineral Dissolution, and Heating on the Nitrogen Isotopic Composition of Fossil-bound Organic Matter</em>", published in the journal <em>Geochemistry, Geophysics, Geosystems</em></p>
Formation of robust bound states of interacting photons
<p>Data and analysis scripts for the manuscript https://arxiv.org/abs/2206.05254</p>
Pin1 two-state structural ensembles of apo, FFpSPR-bound and pCDC25c-bound form
<p>Pin1 is a two-domain cell regulator that isomerizes peptidyl-prolines. The catalytic domain (PPIase) and the other ligand-binding domain (WW) sample extended and compact conformations. Ligand binding changes the equilibrium of the interdomain conformations through an interdomain allosteric mechanism. We have described ligand-specific conformational changes that occur upon binding of pCDC25c and FFpSPR. pCDC25c binding doubles the population of the extended states compared to the virtually identical populations of the apo and FFpSPR-bound forms. pCDC25c binding to the WW domain triggers conformational changes to propagate via the interdomain interface to the catalytic site, while FFpSPR binding displaces a helix in the PPIase that leads to repositioning of the PPIase catalytic loop.</p> <p>Here, we deposit the entire magnetic resonance-based CYANA structure calculation protocols of Pin1 two-state structural ensembles of apo, FFpSPR-bound and pCDC25c-bound form that allowed us to determine the coupling of intra- and interdomain structural sampling Pin1.</p>
Data for: Bounds on the mass of superradiantly unstable scalar fields around Kerr black holes
<p>Datasets associated with the article <strong>Bounds on the mass of superradiantly unstable scalar fields around Kerr black holes</strong>, arXiv:2405.01003 [gr-qc]. The file datasets.zip contains four subfolders. Each subfolder includes a readme file that provides a description of the datasets. A brief description of each subfolder is given below:</p> <p>1) Folder "notebooks" contains minimal Mathematica notebooks that compute scalar clouds and superradiant instabilites of a Kerr black hole</p> <p>2) Folder "clouds" contains data for the mass of the scalar cloud as a function of the spin of the black hole</p> <p>3) Folder "max_instability" contains data for the peak of superradiant instabilities as a function of the spin of the black hole</p> <p>4) Folder "parameters" contains parameters for an analytical function that fits the numerical values of the mass of the scalar clouds of a Kerr black hole </p>
Correlation-based Analysis of the Influence of Bound Constraint Handling Methods on Population Dynamics in Differential Evolution
<p>The dataset is based on the average values collected over 5 independent runs, considering the largest common number of<br>iterations for LSHADE algorithm coupled with ’sat’, ’midT’, ’midB’, ’unif’, ’beta’, ’mir’, ’tor’, ’expC_R’, ’expC_T’, ’expC_B’, ’vectR’, ’vectT’, ’vectB’, ’mahalanobis’ correction methods, on BBOB function f3, 4, 5, 16, 23, instance 1</p> <p>Plots for the averaged values are included for measures 'pop_size', 'best', 'error', 'prob_infeas', 'genMutatedComponent', 'genSuccessMutants','meanImprovements', 'varPop', 'avgF', 'avgCR', 'extension', 'shape', 'eccentricity', 'kl_unif'</p>
IR data of the compounds published in "Bioinspired Nucleophilic Attack on a Tungsten-Bound Acetylene: Formation of Cationic Carbyne and Alkenyl Complexes"
Open the record for dataset details and reuse information.
Data for publication: Unlocking the out-of-plane dimension for photonic bound states in the continuum to achieve maximum optical chirality
Open the record for dataset details and reuse information.
Dataset Inhibition of membrane-bound BAFF by the anti-BAFF antibody belimumab
<p>This dataset is related to "Inhibition of membrane-bound BAFF by the anti-BAFF antibody belimumab" (Kowalczyk-Quintas C, Chevalley D, Willen L, Jandus C, Vigolo M, Schneider P).</p>
Supercurrent-induced Majorana bound states in a planar geometry
<p>Dataset and source code for the paper "Supercurrent-induced Majorana bound states in a planar geometry".</p>
Lower Bound Estimates of WM Capacity dataFiles (Chekaf, Cowan, Mathy)
<p>Data files and R-script used in four experiments of the paper "Lower Bound Estimates of Working Memory Capacity with a Simple Span Task using the Least Compressible Stimulus Lists"</p> <p> </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.