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691 results for “Molecular dynamics”
Fig. 5 in Study of two isoforms of lipoxygenase by kinetic assays, docking and molecular dynamics of a specialised metabolite isolated from the aerial portion of Lithrea caustica (Anacardiaceae) and its synthetic analogs
Fig. 5. Active site of molecular dynamics between 3-pentadecylcatechol (2) (A), (Z)-3-(pentadec-10′-enyl)-catechol (1) (B), and arachidonic acid with 5-hLOX and fluctuation of catechol distances during simulation time (10 ns).
Molecular dynamics dataset of Trypsin-Benzamidine
<p>This dataset contains all-atom molecular dynamics trajectories of Trypsin-Benzamidine. All details regarding the molecular dynamics setup are given in references [1, 2]. The dataset consists of two parts and comes with a time step of 100 ps.</p> <p><strong>long-trajs.tar</strong>: cumulative of 100 µs of MD data in trajectories of 48 x 2 µs and 4 x 1 µs. Generated and used in [1].</p> <p><strong>gpugrid-trajs.tar</strong>: cumulative of 49.5 µs of MD data in trajectories of 495 x 100 ns. Generated for [2] and used in [1, 2].</p> <p>[1] Plattner, N.; Noé, F. Protein Conformational Plasticity and Complex Ligand-Binding Kinetics Explored by Atomistic Simulations and Markov Models. <em>Nature Communications</em> <strong>2015</strong>, <em>6</em>, 7653. <a href="https://doi.org/10.1038/ncomms8653">https://doi.org/10.1038/ncomms8653</a>. </p> <p>[2] Buch, I.; Giorgino, T.; De Fabritiis, G. Complete Reconstruction of an Enzyme-Inhibitor Binding Process by Molecular Dynamics Simulations. <em>Proc. Natl. Acad. Sci. U.S.A.</em> <strong>2011</strong>, <em>108</em> (25), 10184–10189. <a href="https://doi.org/10.1073/pnas.1103547108">https://doi.org/10.1073/pnas.1103547108</a>.</p>
The files for "RlmI-c-di-GMP" molecular dynamics simulation
<p>The crystal structure files (protein RlmI), MD simulation files (input files, parameter files, topology files etc) and structures of c-Di-GMP.</p>
Introduction to HPC: molecular dynamics simulations with GROMACS: input files
<p>Introduction to HPC: molecular dynamics simulations with GROMACS: input files</p>
Identification of novel NLRP3 Inhibitors a comprehensive approach using 2D-QSAR, molecular docking, molecular dynamics simulation and drug-likeness evaluation
<p>This dataset encapsulates the comprehensive outputs derived from molecular docking and molecular dynamics (MD) simulation studies conducted to investigate the binding affinities, interactions, and dynamic behaviors of selected ligands with NLRP3.</p>
Molecular Profiling and Dynamic Changes of ctDNA in Unresectable Locally Advanced NSCLC
ClinicalTrials.gov study NCT05641870. IPD Sharing: UNDECIDED. Countries: 1. Publications: 15.
Chemotherapy, Host Response and Molecular Dynamics in Periampullary Cancer
ClinicalTrials.gov study NCT03724994. IPD Sharing: UNDECIDED. Countries: 1. Publications: 5.
Clinical Efficacy and Molecular Dynamics of Quantum Molecular Resonance (QMR) Electrotherapy in Dry Eye Management
ClinicalTrials.gov study NCT06955806. IPD Sharing: NO. Countries: 1. Publications: 1.
Using Molecular Dynamics Simulations to Interrogate T Cell Receptor Non-Equilibrium Kinetics
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Molecular Dynamics trajectories of the human PDZ2 domain
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Interaction between cytochrome c and DNA: conformation, peroxidase activity and molecular dynamics simulation
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Spatio-temporal dynamics of genetic variation at the quantitative and molecular levels within a natural Arabidopsis thaliana population
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Data from: Molecular dynamics simulation of the interaction between palmitic acid and high pressure CO2
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Supporting data: Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?
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Data from: A molecular phylogeny of forktail damselflies (genus Ischnura) reveals a dynamic macroevolutionary history of female colour polymorphisms
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Data from: Molecular ecology of the Neotropical otter (Lontra longicaudis): non-invasive sampling yields insights into local population dynamics
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Molecular dynamics simulations of the tripartite interface (Syt1_C2B—SNARE—Cpx Complex)
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Molecular dynamics trajectories for ionic conductors in: Paradigms of frustration in superionic solid electrolytes
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Data from: Molecular docking and dynamics studies to identify novel active compounds targeting potential breast cancer receptor proteins from an indigenous herb Euphorbia thymifolia Linn
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Role of black carbon in the formation of primary organic aerosols: Insights from molecular dynamics simulations: Supplementary Materials
<p>This zip file contains supplements for the article entitled "Role of black carbon in the formation of primary organic aerosols: Insights from molecular dynamics simulations" authored by Zhou et al. including three different sets of data as follows:</p> <p>data: Data files that contain optimized atomistic configurations of organic molecules adsorbed on nanoparticles are provided. These .xyz files contain the atomic coordinates of the adsorbed organic molecules. The first line in each file contains the total number of atoms, the second line comprises three integers corresponding to the number of molecules, number of atoms in each molecule and number of atoms in the nanoparticle, and each subsequent line contains the atomic species and the three Cartesian coordinates (in Angstrom) for an atom. Please see the PDF in the directory for instructions.</p> <p>code: Sets of Lammps simulation input scripts.</p> <p>video: Supplements demonstrating the formation process of molecular clusters of these simulations.</p>
ScienceDex guides
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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.