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68 results for “conformational dynamics”
Multiresolution molecular dynamics simulations reveal the interplay between conformational variability and functional interactions in membrane-bound cytochrome 2B4
<p>This dataset contains coordinate files, scripts and input parameters to run and analyse molecular dynamics simulations of membrane bound CYP 2B4.</p> <p> </p> <p>The associated study is described in: </p> <p>data - containes input data & last simulation frames for all of the described MD simulations and analyses described in the manuscript</p> <p>Structures_used_for_figures - contains .pdb and .pse files of all protein structures depicted in the manuscript</p>
Data From: Investigating the Effect of GLU283 Protonation State on the Conformational Heterogeneity of CCR5 by Molecular Dynamics Simulations
<p>This dataset contains MD simulation results for CCR5 receptor in different states. There are three states this GPCR could be in: 1.apo state, i.e. not bound to any other protein or ligand 2.holo state, i.e. bound by maraviroc (MRV) 3.GP120 bound state, i.e. bounded to HIV envelope protein GP120 and human receptor CD4. </p> <p>For apo state simulations, three different starting structure were used and the simulation results for them are given in three different folders named after the PDB ID of initial structures. </p> <p>One critical residue of CCR5 receptor, GLU283, was considered in two different protonation state, hence there are two folders for each studied system, GLU283 and GLH283 for differently protonated systems. </p> <p>The MD trajectories of studied systems are in dcd format and due to size issues waters, ions and membrane atoms were removed. </p> <p>For each system, three replica MD simulations were performed, hence, there are three folders with names REPLICA1, REPLICA2, REPLICA3.</p> <p> </p>
AlphaFold2 Modeling and Molecular Dynamics Simulations of the Conformational Ensembles for the SARS-CoV-2 Spike Omicron JN.1, KP.2 and KP.3 Variants : Mutational Profiling of Binding Energetics Reveals Epistatic Drivers of the ACE2 Affinity and Escape Hotspots of Antibody Resistance
Open the record for dataset details and reuse information.
Raw plasmon ruler data of conformational dynamics of Hsp90
<p>Four time series from Plasmon ruler experiments<br>time resolution 0.1 s.<br>total length 6 h<br>Hsp90 concentration 240 pM<br>First analyzed and published 2018 in: https://pubs.acs.org/doi/10.1021/acs.nanolett.8b03342</p> <p>2024 analyzed for memory in conformational dynamics in: https://arxiv.org/abs/2404.16799</p>
data for "An unbound proline-rich signaling peptide frequently samples cis conformations in Gaussian accelerated molecular dynamics simulations"
<p>Disordered proline-rich motifs are common across the proteomes of many species and are often involved in protein-protein interactions. Proline is a unique amino acid due to the covalent bond between the backbone nitrogen and the proline side chain. The resulting five-membered ring allows proline to sample the <em>cis</em> state about its peptide bond, which other residues cannot do as readily. Because proline-rich disordered sequences exist as ensembles that likely include structures with the proline peptide bond in <em>cis</em>, a robust methodology to accurately account for these conformations in the overall ensemble is crucial. Observing the <em>cis </em>conformations of proline in a disordered sequence is challenging both experimentally and computationally. Nitrogen-hydrogen NMR spectroscopy cannot directly observe proline residues, which lack an amide bond, and computational methods struggle to overcome the large kinetic barrier between the <em>cis </em>and <em>trans </em>states, since isomerization usually occurs on the order of seconds. In the current work, Gaussian accelerated molecular dynamics was used to overcome this free energy barrier and simulate proline isomerization in a tetrapeptide (KPTP) and in the 12-residue proline-rich SH3 binding peptide, ArkA. We found that Gaussian accelerated molecular dynamics, when combined with a lowered peptide bond dihedral angle potential energy barrier (15 kcal/mol), allowed sufficient sampling of the proline <em>cis </em>and <em>trans </em>states on a microsecond timescale. All ArkA prolines spend a significant fraction of time in <em>cis</em>, leading to a more compact ensemble with less polyproline II helix structure than an ArkA ensemble with all peptide bonds in <em>trans</em>. The ensemble containing <em>cis</em> prolines also matches more closely to <em>in vitro</em> circular dichroism data than the all-<em>trans</em> ensemble. The ability of the ArkA prolines to isomerize likely affects the peptide’s ability to bind its partner SH3 domain, and should be studied further. This is the first molecular dynamics simulation study of proline isomerization in a biologically relevant proline-rich sequence that we know of, and a similar protocol could be applied to study multi-proline isomerization in other proline-containing proteins to improve conformational diversity and agreement with <em>in vitro</em> data.</p>
Histone acetylation dynamics modulate chromatin conformation and allele-specific interactions at oncogenic loci.
GEO Series GSE168474. Homo sapiens. 41 samples. Type: Other; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
RNA tertiary structure and conformational dynamics revealed by BASH MaP
GEO Series GSE271825. synthetic construct; Homo sapiens. 26 samples. Type: Other.
Chromatin conformation dynamics during CD4+ Tcell activation implicates autoimmune disease associated genes and regulatory elements (HiC)
GEO Series GSE230342. Homo sapiens. 6 samples. Type: Other.
Dynamic Control of X-Chromosome Conformation and Repression by a Histone H4K20 Demethylase
GEO Series GSE84581. Caenorhabditis elegans. 13 samples. Type: Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing.
Chromatin conformation dynamics during CD4+ Tcell activation implicates autoimmune disease associated genes and regulatory elements (ATAC-Seq)
GEO Series GSE230343. Homo sapiens. 9 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Histone acetylation dynamics modulate chromatin conformation and allele-specific interactions at oncogenic loci (RNASeq)
GEO Series GSE168471. Homo sapiens. 17 samples. Type: Expression profiling by high throughput sequencing.
Tertiary structure and conformational dynamics of the anti-amyloidogenic chaperone DNAJB6b at atomistic resolution
<p>Title of the article - Tertiary structure and conformational dynamics of the anti-amyloidogenic chaperone DNAJB6b at atomistic resolution</p> <p>Here, we have provided the following</p> <ol> <li>Homology models obtained from various software.</li> <li>Configuration files used (*.mdp files)</li> <li>Average structures of closed, open, and extended states obtained from our study. </li> </ol>
Computational insights into the Conformational Dynamics of HIV-1 Vpr in lipid bilayer for ion channel modeling
<p>This is the dataset of input files, parameter files and run files for the various protein conformations generated in the study "Computational insights into the Conformational Dynamics of HIV-1 Vpr in lipid bilayer for ion channel modeling"</p>
Conformation and dynamic interactions of the multipartite genome in Agrobacterium tumefaciens
GEO Series GSE182881. Agrobacterium tumefaciens. 42 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
Chromatin conformation dynamics during CD4+ Tcell activation implicates autoimmune disease associated genes and regulatory elements (RNA-Seq)
GEO Series GSE230345. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
A dynamic folded hairpin conformation is associated with -globin activation in erythroid cells
GEO Series GSE107938. Mus musculus. 3 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Histone acetylation dynamics modulate chromatin conformation and allele-specific interactions at oncogenic loci (ChIPSeq)
GEO Series GSE168472. Homo sapiens. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Conformational dynamics of cohesin/Scc2 loading complex are regulated by Smc3 acetylation and ATP association
GEO Series GSE217833. Saccharomyces cerevisiae. 22 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
A dynamic folded hairpin conformation is associated with -globin activation in erythroid cells
GEO Series GSE107937. Mus musculus. 1 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Histone acetylation dynamics modulate chromatin conformation and allele-specific interactions at oncogenic loci (Hi-C)
GEO Series GSE168470. Homo sapiens. 18 samples. Type: Other.
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Allen Brain Atlas
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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.
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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.
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