Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
691
datasets available to search
ShareScore release 0.7.1
Dataset results
691 results for “Molecular dynamics”
Molecular dynamics dataset for pharmacological repositioning in the treatment of non-small-cell lung cancer
Open the record for dataset details and reuse information.
Data from: Elucidating the impact of red blood cell membrane components on melittin-induced pore formation with molecular dynamics simulations
Open the record for dataset details and reuse information.
Molecular dynamics simulations in: High-resolution structures with bound Mn2+ and Cd2+ map the metal import pathway in an Nramp transporter
Open the record for dataset details and reuse information.
Data for: Optimal inference of molecular interaction dynamics in FRET microscopy
Open the record for dataset details and reuse information.
Molecular dynamics simulation data of ELIC in nanodiscs
Open the record for dataset details and reuse information.
Molecular dynamics simulation files for: a molecular machine efficiently drives glycosaminoglycan assembly and secretion for osteoarthritis therapy
Open the record for dataset details and reuse information.
Molecular dynamics simulation of Conus textile conotoxin Txd13 in complex with a3b2, a3b4, a6b2 or a6b4 nAChR subtypes.
<p>This folder contains the coordinate and parameter files used to run molecular dynamics simulations of the toxin Txd13 (sequence GCCSNPPCIANPMC) in complex with four nicotinic acetylcholine receptor (nAChR) subtypes: a3b2, a3b4, a6b2 and a6b4 nAChRs. For each system several files are provided:</p> <p>1) an homology model that was used as a starting conformation is provided (eg 'a3b2_txd13.B99990023.pdb'),<br> 2) an Amber Parm7 topology file (eg 'a3b2_txd13_0023.prmtop'),<br> 3) a trajectory files containig 1250 frames extracted from a 100 ns molecular dynamics simulation (eg 'a3b2_txd13_0023_md_smaller.nc') created using pmemd from the Amber 18 package,<br> 4) the log file of this simulations (eg 'a3b2_txd13_0023_md.log'), and<br> 5) the coordinate file representing the minimized verion of the centroid frame of each simulation (with water and ions removed for conveniance) (eg 'a3b2_txd13_0023_md_centroid_min_nowat.pdb')</p> <p>The parameters used for the molecular dynamics simulations are provided in the 'md.in' file.</p> <p>All the text files have been compressed in the 'xz' format</p>
Files for Molecular Dynamics Simulation of COSAN
<p>Topology file (.top), force field parameters file (.prm) and coordinate file (.pdb) for Molecular Dynamics Simulations of COSAN molecule compatible with CHARMM force field. Files based on the parameters reported in:</p> <p>D.C. Malaspina, C. Viñas, F. Teixidor, J. Faraudo "Atomistic Simulations of COSAN: Amphiphiles without a Head-and-Tail Design Display “Head and Tail” Surfactant Behavior", Angewandte Chemie International Edition Vol 59(8), Pages 3088-3092 (2020)</p> <p>DOI: <a href="https://doi.org/10.1002/anie.201913257">10.1002/anie.201913257</a></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>
Supplemental Materials for "Formation of interstellar complex polycyclic aromatic hydrocarbons: Insights from molecular dynamics simulations of dehydrogenated benzene"
<p>Supplemental Materials for the article entiled "Formation of interstellar complex polycyclic aromatic hydrocarbons: Insights from molecular dynamics simulations of dehydrogenated benzene" authored by M. Hanine et al. at Laboratory for Relativistic Astrophysics, Department of Physics, Guangxi University, 530004 Nanning, China.</p> <p>email: zw@gxu.edu.cn (Zhao Wang)</p> <p>SuppMater1.zip :</p> <p>Atomistic configurations of the formed PAH molecules (in 4.0 ns) at all studied temperatures are available in .xyz format. These .xyz files contain the atomic coordinates of the formed molecules by giving the total number of atoms that will be read on the first line; the comment text on the second; and the atomic number and three atomic Cartesian coordinates in the following lines. The name of the .xyz file consists of four parts separated by ``\_'' including the source molecule type, the temperature, the formation environment (with NP or in gas phase), and the molecular ID (among multiple molecules formed in a simulation). For instance, ``C6H2\_300K\_gas\_2.xyz'' stands for the 2nd molecule formed from C6H at 300K in the gas phase. Please read the 'readme.txt' file before using the data.</p> <p> </p> <p>SuppMater2.pdf:</p> <p>A data file that contains the DFT-calculated optimized structures and their atomic coordinates.</p> <p> </p> <p>SuppMater3.mp4:</p> <p>An animation demonstrating the formation process of PAHs on a carbon NP.</p>
Interaction between cytochrome c and DNA: conformation, peroxidase activity and molecular dynamics simulation
A mixed system of cytochrome c (Cyt c, a typical hemoprotein) and DNA was constructed and the interaction between Cyt c and DNA were analyzed by experiment and molecular dynamics (MD) simulation methods, respectively. On the one hand, the experimental results showed: 1. The peroxidase activity of the mixed system was significantly enhanced relative to the Cyt c in 50 mM phosphate buffer solution at 25ºC. 2. UV-Vis spectra study found that, compared with the Cyt c solution, the absorbance of the Cyt c-DNA mixed system increased significantly at 280 nm, while the absorbance decreased at 405 nm, indicating that the overall structure of Cyt c in the mixed system became loose, and the structure around heme group became more compact. 3. Circular Dichroism (CD) studies showed that there was a weak interaction between DNA and Cyt c in the mixed system, which had little effects on the secondary structures of Cyt c. On the other hand, MD simulation results showed: 1. DNA and Cyt c were combined by hydrogen bonding and non-bonding interactions in the mixed system. 2. During the simulation process, N-Terminal α-Helix changed, and Lys13-Cys17 opened, exposing the active center (heme structure) of Cyt c, which may increase the binding of the mixed system to the substrate. 3. The bond length of Fe-N (N in His18 and Fe in heme group) became slightly shorter after equilibrium in the presence of DNA. 4. The Cyt c became loose after binding with DNA. 5. The total binding free energy between Cyt c and DNA was calculated to be -141.9 kJ/mol. The Cyt c-DNA system was in a relatively stable state from energy perspective. The results of the research on the structure and function of the Cyt c-DNA mixed system using experimental method and MD simulation method were consistent. The combination of experimental method and simulation method may provide useful research ideas and effective research methods for further studying the interaction mechanism between hemeprotein and DNA.
N-ASW: Molecular Dynamics Data
<ul> <li> Description</li> </ul> <p>The data set was generated from ab-initio molecular dynamics simulations and was used to study the adsorption and desorption dynamics of nitrogen atoms on top of amorphous solid water (ASW) [1]. The data set contains structures with 3 to 378 atoms which result in 28,715 structures in total. The atomization energies and atomic forces are calculated at the PBEh-3c/def2-mSVP level of theory [2]. For more details, see Ref. 1.</p> <ul> <li> Format</li> </ul> <p>The data is stored in python compressed array format (.npz) with the atomization energy in kcal/mol and atomic forces in kcal/mol/Ang. The data set contains five numpy arrays</p> <p>import numpy as np<br> data = np.load('N-ASW.npz')<br> data['R'] # Cartesian coordinates of nuclei (Ang.)<br> data['E'] # Total energy (kcal/mol)<br> data['F'] # Atomic forces (kcal/mol/Ang.)<br> data['N'] # Number of atoms in each structure<br> data['Z'] # Nuclear charges</p> <ul> <li>References</li> </ul> <p>[1] Molpeceres G.; Zaverkin V.; and Kästner J. Neural-Network Assisted Study of Nitrogen Atom Dynamics on Amorphous Solid Water. I. Adsorption & Desorption. Mon. Not. R. Astron. Soc. 2020, submitted<br> [2] Grimme S.; Brandenburg J. G.; Bannwarth C.; Hansen A. Consistent structures and interactions by density functional theory with small atomic orbital basis sets. J. Chem. Phys. 2015, 143, 054107.</p>
Dataset for "Strain induced electrochemical behaviours of ionic liquid electrolytes in an electric double layer capacitor: Insights from molecular dynamics simulations"
<p>The datafile contains molecular dynamics simulation results for analysing the electrochemical behaviour of ionic liquid based EDLC under compression and tension.</p>
Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
<p>A dye-sensitized solar cell was solvated by RTILs; using optimized empirical potentials, a molecular dynamics simulation was applied to compute vibrational properties. The obtained vibrational spectra were compared with experiment and ab initio molecular dynamics; various empirical potential spectra show how partial-charge charge parameterization of the ionic liquid affects vibrational spectra prediction.</p>
Molecular dynamics trajectories for ionic conductors in: Paradigms of frustration in superionic solid electrolytes
<p>Superionic solid electrolytes have widespread use in energy devices, but the fundamental motivations for fast ion conduction are often elusive. Here, we draw upon atomistic simulations of a wide range of halide, oxide, sulfide, and <em>closo</em>-borate superionic conductors to illustrate some of the key features that enhance local cation mobility in these solids. We classify three types of frustration that create competition between different local atomic preferences, thereby flattening the diffusive energy landscape and enhancing entropy. These include chemical frustration, which derives from competing factors in the anion-cation interaction; structural frustration, which is connected to the lack of a clear site preference for mobile ion ordering; and dynamical frustration, which is associated with temporary fluctuations in the energy landscape due to anion orientations or cation reconfigurations. For each class of frustration, we provide detailed simulation analyses of multiple materials to show how ion mobility is facilitated, resulting in stabilizing factors that are both entropic and enthalpic in origin. Implications for identifying suitable descriptors for superionic conductivity are discussed.</p>
Data from: Molecular ecology of the Neotropical otter (Lontra longicaudis): non-invasive sampling yields insights into local population dynamics
Non-invasive genetic analysis has been frequently employed to estimate ecological and population parameters for many secretive and/or threatened species. However, Neotropical carnivores have so far been scarcely targeted by such studies. The Neotropical otter (Lontra longicaudis) is a poorly-known species for which local levels of genetic diversity and demographic parameters are virtually absent. We employed non-invasive sampling and amplification of microsatellite loci to investigate population size and density, spatial organization, and relatedness of a wild Neotropical otter population in an Atlantic forest area in southern Brazil. We directly identified 28 individuals and estimate a rather high population density at the study site. Spatial organization analysis indicated that male cumulative displacement was higher than that of females, with the latter sex showing evidence of philopatric behaviour. Also, the reconstruction of genealogical relationships suggests that spatial organization in this otter appears to be influenced by relatedness. By allowing the testing of specific hypothesis targeting these issues, our results provided important glimpses into the Neotropical otter's population biology. Moreover, the findings of the present study reaffirm the power of non-invasive genetics to investigate the biology of this elusive species, and open up new avenues for ecological and demographic studies of other Neotropical carnivores.
Molecular dynamics simulations of the temperature-induced unfolding of crambin follow the Arrhenius equation
<p>These are the files needed to carry out the temperature induced infolding of crambin using Gromacs.</p>
Multiscale molecular dynamics simulations of human P-glycoprotein in complex lipid bilayer
<p>The topology (gro) and trajectory (xtc) files for multiscale - coarse-grained (CG) and atomistic (AT) molecular dynamics simulations of human P-glycoprotein in complex lipid bilayer. The coarse grained simulations are 10 microseconds long and the trajectories have 1 frame saved at every 10 ns, while the atomistic simulations are 100 ns long and have 2 frames saved at every nanosecond. </p>
Molecular dynamics trajectory videos for high-affinity short peptides targeting BamA protein of Candidatus liberibacter asiaticus
<p>Molecular dynamics trajectory videos and trajectory analysis reports for high-affinity short peptides targeting BamA protein of <em>Candidatus</em> liberibacter asiaticus</p>
The dynamics of protein-RNA interfaces using all-atom molecular dynamics simulations
<p>We investigated to characterize the dynamics of protein-RNA complexes and their interfaces at molecular level by performing a more systematic analysis. To get insights on the dynamics of protein-RNA complexes, all-atom MD simulations were generated for the manuscript "The dynamics of protein-RNA interfaces using all-atom molecular dynamics simulations". Nine protein-RNA complexes are studied in this work: 1ASY (an aspartyl-tRNA synthase/tRNA), 1JBS (a ribotoxin restrictocin/SRD RNA), 1MMS (a ribosomal protein L11/23S), 1OOA (a nuclear factor NF-kappaB p105 subunit/RNA aptamer), 1RKJ (a nucleolin/pre-rRNA), 2R8S (a FAB/P4-P6 RNA ribozyme domain), 2VPL (a 50S ribosomal protein/mRNA), 2ZM5 (a tRNA delta(2)-isopentenylpyrophosphate transferase/tRNA), 3IEV (a GTP-binding protein era/3' end of 16S rRNA). </p><p>Each folder for a complex is organised as followed:</p><ul><li>in <strong>complex</strong> there are the dry MD simulations for the complex protein-RNA with the starting structure</li><li>in <strong>protein</strong> there are the dry MD simulations for the unbound protein with the starting structure</li><li>in <strong>rna</strong> there are the dry MD simulations for the unbound RNA with the starting structure</li></ul><p>In each folder, all the trajectory files are named : <strong>md_(times of simulations).xtc</strong> and the starting structure called : <strong>start.gro</strong>.</p>
ScienceDex guides
Understand access before you commit
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.