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.
5
datasets available to search
ShareScore release 0.9.0
Dataset results
5 results for “Implicit solvent”
Replica exchange molecular dynamics simulation data of designed β-hairpins (implicit solvent, AMBER ff96)
<p>Raw REMD simulation data (protein only) of designed β-hairpins. AMBER ff96 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>
Replica exchange molecular dynamics simulation data of designed β-hairpins (implicit solvent, AMBER ff99SB-ildn)
<p>Raw REMD simulation data (protein only) of designed β-hairpins. AMBER ff99SB-ildn 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>
Alanine dipeptide in an implicit solvent at 300K
<p>This dataset has been introduced in the article <a href="https://arxiv.org/abs/2208.01893">Midgley, et al.: Flow Annealed Importance Sampling Bootstrap, 2022</a>.</p> <p>It contains samples from the Boltzmann distribution of alanine dipeptide in an implicit solvent, which have been generated with a Replica Exchange Molecular Dynamics (REMD) simulation. The ff96 with an OBC GBSA implicit solvent was used.</p> <p>The REMD uses 21 replicas starting at a temperature of 300K and increasing the temperature by an increment of 50K. The replicas are exchanged every 200 iterations and use the state at each multiple of 1000 time steps as samples. Many of these simulations were in parallel with different seeds. We let the system equilibrate for <span class="math-tex">\(2\times10^5\)</span> iterations and run the simulation subsequently for <span class="math-tex">\(2\times10^6\)</span> iterations.</p> <p>The data is split into a training set, which consists of <span class="math-tex">\(10^6\)</span> samples; a validation set consisting of <span class="math-tex">\(10^6\)</span> samples as well; and a test set with <span class="math-tex">\(10^7\)</span> samples.</p> <p>The data is provided as raw <span class="math-tex">\((x,y,z)\)</span>-coordinates, stored as *.h5 files, and transformed to internal coordinates, stored as *.pt files.</p> <p>More details about the data and how to use it are given in our <a href="https://github.com/lollcat/fab-torch">GitHub repository</a> and <a href="https://arxiv.org/abs/2208.01893">paper</a>.</p>
Molecular dynamics simulation trajectories for the GB99dms implicit solvent force field
<p>Molecular dynamics simulation trajectories used in training and validating the GB99dms implicit solvent protein force field. See the paper:</p> <ul> <li>Greener JG. Differentiable simulation to develop molecular dynamics force fields for disordered proteins, <a href="https://doi.org/10.1039/D3SC05230C" target="_blank" rel="noopener">Chemical Science</a> 15, 4897-4909 (2024)</li> </ul> <p>For more information, including structure files for these trajectories, see https://github.com/greener-group/GB99dms.</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>
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.