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56 results for “virtual screening”
Machine Learning Guided AQFEP: A Fast & Efficient Absolute Free Energy Perturbation Solution for Virtual Screening
<p>Data to reproduce primary figures in the manuscript titled: Machine Learning Guided AQFEP: A Fast & Efficient Absolute Free Energy Perturbation Solution for Virtual Screening.</p> <p>URL: https://chemrxiv.org/engage/chemrxiv/article-details/6583785e66c1381729ac86f5</p>
PROTAC virtual screening: A retrospective screening exercise
<p>My goal is to test whether retrospective virtual screening approaches can guide the design of PROTACs. As a first step, I showed that HADDOCK was the best protein-protein docking tool among those I tested to predict how E3 ligases interact with their protein substrates. Here, I ask whether docking virtual libraries of PROTAC candidates to these E3 ligase – substrate protein interfaces can be used to predict which PROTACs are active.</p>
PIGNet2: A versatile deep learning-based protein-ligand interaction prediction model for accurate binding affinity scoring and virtual screening
<p>Training and test datasets of the paper "Improving the versatility of deep learning-based protein-ligand interaction prediction for accurate binding affinity scoring and virtual screening".</p>
Identification of Potential JNK3 Inhibitors Through Virtual Screening, Molecular Docking And Molecular Dynamics Simulation as Therapeutics for Alzheimer's Disease
<p>Alzheimer's disease (AD) is a complex neurological disorder without effective treatment. One factor in its development is c-Jun N-terminal kinases (JNKs), a type of protein related to brain function. JNK3, found mainly in the brain, contributes to AD by promoting brain abnormalities. Current research aims to create new JNK3 inhibitors for AD treatment using a virtual screening method. A database of compounds was filtered, and five potential compounds were identified with better scores than a reference. These compounds underwent simulations and energy calculations, showing stability and potential as JNK3 inhibitors.</p>
Large scale virtual screening for finding inhibitor against the main protease from herbal medicine for SARS-Cov2 therapy
Open the record for dataset details and reuse information.
Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity
Open the record for dataset details and reuse information.
Virtual screening for functional foods against the main protease of 2019 novel coronavirus
<p>Design and development of an effective method or technologyto combat the 2019 novel coronavirus remains a challenge. In this work, the special attention was paid on the interaction between functional foods and the main protease of 2019-nCoV. Here, 10870 ligands were employed and screened by the molecular docking, which involved 12 kinds of functional foods (carbohydrates, fat acids, phospholipids, vitamin, β-sitosterol, flavonoids, nordihydroguaiaretic acid, curcumin, nookatone, β-pinene, tincturoid, and their isomers/analogs/derivatives). Then, 60 ligands were obtained with the good docking affinity. Most of them belong to quercetin and its isomers/analogs/derivatives, which also showed the highest affinity for the main protease of 2019-nCoV. The dynamic simulation indicated that quercetin-protease and quercetin-analog-protease showed the excellent stability. Thus, quercetin may be the best candidate to prevent or inhibit the main protease of 2019-nCoV. Considering the green and white tea are rich in quercetin and its isomers/analogs/derivatives, tea and relative beverages may become a good option to regulate our metabolism and help us to overcome this special time.</p>
Identification of Potential IL4I1 Inhibitors through Structure-Based Virtual Screening and Molecular Dynamics Simulations, Molecular dynamics trajectory file
<p>Dataset for molecular dynamics simulations of the article: Identification of Potential IL4I1 Inhibitors through Structure-Based Virtual Screening and Molecular Dynamics Simulations.</p> <p><a href="../api/records/10473570/draft/files/First_600ns_MD.rar/content" target="_blank" rel="noopener noreferrer">First_600ns_MD.rar</a> contains the 600ns molecular dynamics simulation trajectory file of IL4I1-FAD-CIT complex using desmond.</p> <p><a href="../api/records/10473570/draft/files/Second_500ns_MD_ZL35_F963.rar/content" target="_blank" rel="noopener">Second_500ns_MD_ZL35_F963.rar </a>contains the 500ns molecular dynamics simulation trajectory file of IL4I1-FAD-ZL35 complex, which initial conformation of this part of dynamics simulation was obtained by docking the conformation of the 963rd frame from the first dynamics simulation with ZL35 through induced fit.</p> <p>script.rar include scripts and calculation methods for free energy landscape, RMSD matrix, and thermol MM/GBSA.</p>
Supporting Information for Cholinergic Selectivity of FDA-approved and Metabolite Compounds Examined with Molecular Docking-based Virtual Screening
<p><span>Typical docking configurations, detailed docking and visualization results for representative ligands and proteins. </span></p>
Virtual Screening and Testing of GSK-3 Kinase Inhibitors Using human SH-SY5Y Neuronal cells Expressing Tau Folding Reporter and Mouse Hippocampal Primary Neuron Culture Under Tau Cytotoxicity
<p>Supplementary Figure S1. for IJMS</p>
Virtual screening of the Janssen compound collection against SARS-CoV-2 Mpro
<p>This short report describes the most relevant results of virtually screening the Janssen Pharmaceutica compound collection for potential activity against SARS-CoV-2 Mpro and confirmation of potential hits in a VeroE6 cell-based anti-SARS-CoV-2 assay.</p>
Virtual screening of the Enamine REAL database against SARS-CoV-2 RdRP
<p>This short report describes the most relevant results of virtually screening the Enamine REAL database for potential activity against SARS-CoV-2 RdRP and confirmation of potential hits in a VeroE6 cell-based anti-SARS-CoV-2 assay.</p>
Virtual screening of 2629 Janssen compounds against SARS-CoV-2 RdRP
<p>This short report describes the most relevant results of virtually screening the Janssen Pharmaceutica compound collection for potential activity against SARS-CoV-2 RdRP and confirmation of potential hits in a VeroE6 cell-based anti-SARS-CoV-2 assay.</p>
Virtual screening on SARS-CoV-2 Nsp14_testing of 5474 hits in a Nsp14 biochemical assay and an A549-hACE2 SARS-CoV-2 infected cells
<p> </p> <p>This report describes the most relevant results of virtually screening the Janssen Pharmaceutica compound collection for potential activity against SARS-CoV-2 Nsp14 and confirmation of potential hits in a SARS-CoV-2 Nsp10/Nsp14 biochemical exonuclease assay and in a A549-hACE2 cell-based anti-SARS-CoV-2 assay.</p>
Identification of Mitoxantrone as a Potent Inhibitor of Transcriptional Cyclin-Dependent Kinase 7 via Structure-based Virtual Screening
<p>Data associated with the manuscript - Identification of Mitoxantrone as a Potent Inhibitor of Transcriptional Cyclin-Dependent Kinase 7 via Structure-based Virtual Screening </p>
Virtual screening data sets for fragmented interaction fingerprint
<p>Data sets containing docking poses, structure-activity relationship matrix (SARM) train-test splitting, and 2048 bits extended connectivity fingerprint (ECFP) descriptors for six biological targets. Poses were generated by employing molecular docking using Molecular Operating Environment (MOE) software. Details will be described in the original publication.</p>
Anti-Riok2 virtual screening output results
<p>Various investigations have revealed the role of RIOK2 in the carcinogenesis and potential of RIOK2 inhibitors as anticancer medicine. In this study, an in-silico approach have been utilized to find potential RIOK2 inhibitors and the uplouded file is the output of docking based virtual screening.</p>
Colon Capsule Versus Virtual Colonoscopy for Colorectal Cancer Screening
ClinicalTrials.gov study NCT02558881. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Virtual Colonoscopy (VC) for Primary Colorectal Screening
ClinicalTrials.gov study NCT00204867. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Screening for Colorectal Cancer With FOBT, Virtual Colonoscopy and Optical Colonoscopy. A Randomized Clinical Trial in the Florence District
ClinicalTrials.gov study NCT01651624. IPD Sharing: Not stated. Countries: 1. Publications: 2.
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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)
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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.