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Layout of the structure for identifier minting workflow published on KNIME ... Open Access
Published: 09 December 2025
Figure 1.
Layout of the structure for identifier minting workflow published on KNIME Community Hub.
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Layout of the structure for KNIME annotation workflow published on KNIME Co... Open Access
Published: 09 December 2025
Figure 2.
Layout of the structure for KNIME annotation workflow published on KNIME Community Hub.
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Example dashboard output using the KNIME annotation tool for a single compo... Open Access
Published: 09 December 2025
Figure 5.
Example dashboard output using the KNIME annotation tool for a single compound, Diclofenac sodium.
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Tazarotene; chemical, pharmaceutical, and biochemical information taken fro... Open Access
Published: 09 December 2025
Figure 12.
Tazarotene; chemical, pharmaceutical, and biochemical information taken from the ChEMBL Annotation Dashboard.
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Overlap of druggable proteome in Homo sapiens between the R4A set and ChEMB... Open Access
Published: 09 December 2025
Figure 16.
Overlap of druggable proteome in Homo sapiens between the R4A set and ChEMBL chemical compounds for targets associated with clinical compounds. (a) Overall overlap of UniProt IDs; (b) overlap of UniProt IDs by target class. Count is based on the number of unique UniProt IDs, considering binding and
Journal Article
From library to landscape: integrative annotation workflows for compound libraries in drug repurposing Open Access
Database, Volume 2025, 2025, baaf081, https://doi.org/10.1093/database/baaf081
Published: 09 December 2025
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Neo4j dashboard. (a) compound search panel, (b) compound’s analogues space ... Open Access
Published: 09 December 2025
Figure 6.
Neo4j dashboard. (a) compound search panel, (b) compound’s analogues space search panel, (c) target search panel.
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Compound-centric information retrieved by the KNIME and Python annotation p... Open Access
Published: 09 December 2025
Figure 7.
Compound-centric information retrieved by the KNIME and Python annotation pipelines (blue and red bars, respectively). The similarity between the two sets was measured using the Jaccard Index (black line). Data from binding and functional assays with a pChEMBL value ≥ 6 and a confidence score ≥ 8 we
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(a) ChEMBL protein family classification from KNIME’s annotation; (b) ChEMB... Open Access
Published: 09 December 2025
Figure 9.
(a) ChEMBL protein family classification from KNIME’s annotation; (b) ChEMBL protein family classification from Python’s annotation. Data from binding and functional assays with a pChEMBL value ≥ 6 and a confidence score ≥ 8 were considered.
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Distribution of compounds from the R4A set indicating the number of targets... Open Access
Published: 09 December 2025
Figure 11.
Distribution of compounds from the R4A set indicating the number of targets in Homo sapiens they are reported to be active against. Data from binding and functional assays with a pChEMBL value ≥ 6 and a confidence score ≥ 8 were considered.
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Profiles of pharmaceutical, clinical, and biological results retrieved from... Open Access
Published: 09 December 2025
Figure 13.
Profiles of pharmaceutical, clinical, and biological results retrieved from the ChEMBL Annotation Dashboard for (a) Ezogabine (Retigabine) and (b) JNJ-37822681.
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Comparison between the R4A set (orange) and the ChEMBL clinical compounds (... Open Access
Published: 09 December 2025
Figure 15.
Comparison between the R4A set (orange) and the ChEMBL clinical compounds (blue); (a) R4A set has ∼20% overlap of ChEMBL IDs with all ChEMBL clinical compounds, (b) violin plots of maximum Tanimoto similarity of ChEMBL clinical compounds with R4A set using MACCS (blue), Morgan radius 2 (green), and
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Overview of the KNIME and Python annotation workflows. (a) KNIME pipeline: ... Open Access
Published: 09 December 2025
Figure 4.
Overview of the KNIME and Python annotation workflows. (a) KNIME pipeline: In the workflow, we make use of both PubChem and ChEMBL databases to aggregate all relevant biological and chemical information, (b) Python pipeline: different molecular identifiers (SMILES, InChI, and InChIKey) can be used a
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Annotation-centric information retrieved by the KNIME and Python annotation... Open Access
Published: 09 December 2025
Figure 8.
Annotation-centric information retrieved by the KNIME and Python annotation pipelines (blue and red bars, respectively). The similarity between the two sets was measured using the Jaccard Index (black line). Data from binding and functional assays with a pChEMBL value ≥ 6 and a confidence score ≥ 8
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(a) Most frequently active reported targets in ChEMBL database for the R4A ... Open Access
Published: 09 December 2025
Figure 10.
(a) Most frequently active reported targets in ChEMBL database for the R4A set (i.e. number of pChEMBL values per target); (b) top-ranked targets based on the number of unique compounds. Data from binding and functional assays with a pChEMBL value ≥ 6 and a confidence score ≥ 8 were considered.
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Target space graph plot of domperidone and its analogues generated from the... Open Access
Published: 09 December 2025
Figure 14.
Target space graph plot of domperidone and its analogues generated from the ‘Compound’s analogue space search’ page of the Chemical Biology Atlas.
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Comparison between the R4A set (orange) and Drug Repurposing Hub (yellow). ... Open Access
Published: 09 December 2025
Figure 17.
Comparison between the R4A set (orange) and Drug Repurposing Hub (yellow). (a) Violin plots of Maximum Tanimoto similarity of Drug Repurposing Hub compounds with R4A set using MACCS (blue), Morgan radius 2 (green) and FeatMorgan radius 2 (orange) fingerprints, (b) PCA on physico-chemical properties
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Screenshot illustrating an example of target exploration in the HCoVDB data... Open Access
Published: 26 November 2025
Figure 4.
Screenshot illustrating an example of target exploration in the HCoVDB database. (A) Basic information on the SARS-CoV-2 protein NSP1. (B) Options to view detailed molecular docking results by selecting the drug ‘Montelukast’.
Journal Article
Automated annotation and validation of human respiratory virus sequences using VADR Open Access
Database, Volume 2025, 2025, baaf078, https://doi.org/10.1093/database/baaf078
Published: 26 November 2025
