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60 results for “Computational Design”
Table A6 images from Computer-aided drug design (CADD) to de-orphanise marine molecules: Finding potential therapeutic agents for neurodegenerative and cardiovascular diseases
<p>High Reslution Images from Table A6</p>
Massively parallel, computationally-guided design of a pro-enzyme
<p>Confining the activity of a designed protein to a specific microenvironment would have broad-ranging applications, such as enabling cell type-specific therapeutic action by enzymes while avoiding off-target effects. While many natural enzymes are synthesized as inactive zymogens that can be activated by proteolysis, it has been challenging to re-design any chosen enzyme to be similarly stimulus-responsive. Here, we develop a massively parallel computational design, screening, and next-generation sequencing-based approach for pro-enzyme design. As a model system, we employ carboxypeptidase G2 (CPG2), a clinically approved enzyme that has applications in both the treatment of cancer and controlling drug toxicity. Detailed kinetic characterization of most effective designed variants shows that they are inhibited by approximately 80% compared to the unmodified protein, and their activity is fully restored following incubation with site-specific proteases. Introducing disulfide bonds between the pro- and catalytic domains based on the design models increases the degree of inhibition to 98%, but decreases the degree of restoration of activity by proteolysis. A selected disulfide-containing pro-enzyme exhibits significantly lower activity relative to the fully activated enzyme when evaluated in cell culture. Structural and thermodynamic characterization provides detailed insights into the pro-domain binding and inhibition mechanisms. The described methodology is general and could enable the design of a variety of pro-proteins with precise spatial regulation.</p>
Data for "Computational Design of Alloy Nanostructures for Optical Sensing of Hydrogen"
<p>This record contains data pertaining to the publication "Computational Design of Alloy Nanostructures for Optical Sensing of Hydrogen".</p>
Supplementary Materials: Next Generation Computational Tools for the Modeling and Design of Particle Accelerators at Exascale
<p>Supplementary materials (aka data artifact or data archive) for our NAPAC22 publication: "Next Generation Computational Tools for the Modeling and Design of Particle Accelerators at Exascale" (Paper ID: TUYE2).</p> <p>Work supported by the Exascale Computing Project (17-SC-20-SC), a joint project of the U.S. Department of Energy's Office of Science and National Nuclear Security Administration, responsible for delivering a capable exascale ecosystem, including software, applications, and hardware technology, to support the nation's exascale computing imperative. This work was supported by the Laboratory Directed Research and Development Program of Lawrence Berkeley National Laboratory under U.S. Department of Energy Contract No. DE-AC02-05CH11231.<br> This research used resources of the National Energy Research Scientific Computing Center (NERSC), a U.S. Department of Energy Office of Science User Facility located at Lawrence Berkeley National Laboratory, operated under Contract No. DE-AC02-05CH11231.</p>
Computational Strategies for Designing Bidentate Hypervalent Iodine Catalysts in Halogen Bond-Mediated Organocatalysis
<p>Computational Strategies for Designing Bidentate Hypervalent Iodine Catalysts in Halogen Bond-Mediated Organocatalysis</p> <p>Email: cristina.trujillodelvalle@manchester.ac.uk</p> <p> </p> <p>Please find the supporting information for the "Computational Strategies for Designing Bidentate Hypervalent Iodine Catalysts in Halogen Bond-Mediated Organocatalysis" paper here.</p>
Multi-Scale Computational Design of Metal-Organic Frameworks for Carbon Capture Using Machine Learning and Multi-Objective Optimization
<p>This repository contains CIF files for metal-organic frameworks and Grand canonical Monte Carlo (GCMC) simulation results for the article <em>Multi-Scale Computational Design of Metal-Organic Frameworks for Carbon Capture Using Machine Learning and Multi-Objective Optimization</em> by Zijun Deng and Lev Sarkisov.</p>
Dataset of Easy screen P300 speller brain–computer interface design
<p><span>This study tested an application on 30 subjects, comprising 11 healthy women and 19 healthy men. Brain signals were recorded using a Brain Products V-Amp 16 Channel EEG system, with electrodes positioned according to the International 10-20 system. The signals were filtered using a 1-12 Hz Butterworth band-pass and a 50 Hz Notch filter, then digitized at a sampling frequency of 2 kHz and transferred to a computer for further analysis.</span></p>
The data of the mesh used in: Pan M, Zou R, Jüttler B. Algorithms and Data Structures for Cs-smooth RMB-splines of Degree 2s+ 1. Computer Aided Geometric Design, 2024: 102389.
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Use of Computer Aided Design and 3D Printing for Anesthesiology Management in a Pediatric Patient With Cleft Facial Defect (3D Obturator) - Pilot Trial
ClinicalTrials.gov study NCT04422964. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Study of Provider Computer Alerts Designed to Improve Delivery of HIV Care
ClinicalTrials.gov study NCT00678600. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Use of Computer Aided Design and 3D Printing for Anesthesiology Management in a Pediatric Patient With Cleft Facial Defect
ClinicalTrials.gov study NCT04422847. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Investigation of the Effect of Deep Margin Elevation Technique on the Clinical Performance of Endocrown Restorations Produced by Computer-Aided Design and Computer-Aided Manufacturing (CAD/CAM) System
ClinicalTrials.gov study NCT06222918. IPD Sharing: UNDECIDED. Countries: 1. Publications: 2.
Data from: How large spatially-explicit optimal reserve design models can we solve now? an exploration of current models’ computational efficiency
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Data from: Computational design of protein-based inhibitors of Plasmodium vivax subtilisin-like 1 protease
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Computer-aided solvent mixture design for the crystallisation and isolation of mefenamic acid
<p>The files contain the MINLP formulations presented in this publication.</p> <p>The MINLP problems are implemented and solved in GAMS version 28.2.0, using SBB, a local branch-&-bound MINLP solver.</p>
Computer-aided solvent mixture design for the crystallisation and isolation of mefenamic acid
<p>The files contain the MINLP formulations presented in this publication.</p> <p>The MINLP problems are implemented and solved in GAMS version 28.2.0, using SBB, a local branch-&-bound MINLP solver.</p>
Computer Aided Design (CAD) files for capillaric circuit with 4 retention burst valves
<p>AutoCAD design file and STL file for capillaric circuit with 4 retention burst valves.</p>
Computational design of the temperature optimum of an enzyme reaction
<p>This repository accompanies the following publication: (added upon publication)</p> <p>EVB.zip contains input files for simulations performed with Q. It contains a topology file, a fep file and a input files used to perform minimization, equilibration and FEP/EVB simulations on a psychrophilic amylase. The version of Q used in this research is also available on Zenodo: <span>10.5281/zenodo.7940182</span></p> <p>Fig_2.zip contains raw data and python code used to generate the subplots shown in figure 2 in the publication. The python code is in the form of an ipython notebook.</p>
Design and Evaluation the Effects of Kinect-based Computer Games for U/E Training in Chronic Stroke Patients
ClinicalTrials.gov study NCT03229733. IPD Sharing: NO. Countries: 0. Publications: 3.
A computer-guided design tool to increase the efficiency of cellular conversions
GEO Series GSE165961. Homo sapiens. 64 samples. Type: Expression profiling by high throughput sequencing.
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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.