ArticleBioinformatics (Oxford, England)2018
Orthologue chemical space and its influence on target prediction.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
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- A Computational Approach to Identify Novel Protein Targets Uncovers New Potential Mechanisms of Action of Mirtazapine S(+) and R(-) Enantiomers in Rett Syndrome.Journal of neurochemistry · 2025Article
- Exploring the Antimycobacterial Potential of Podocarpusflavone A fromPharmaceuticals (Basel, Switzerland) · 2024Article
- The workshops on computational applications in secondary metabolite discovery (CAiSMD).Physical sciences reviews · 2024Review
- Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank.Journal of chemical information and modeling · 2024Article
- Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA DICTrank.bioRxiv : the preprint server for biology · 2023Article
- Design and Synthesis of New Anthranyl Phenylhydrazides: Antileishmanial Activity and Structure-Activity Relationship.Pharmaceuticals (Basel, Switzerland) · 2023Article
- Mechanism of action deconvolution of the small-molecule pathological tau aggregation inhibitor Anle138b.Alzheimer's research & therapy · 2023Article
- EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022.Nucleic acids research · 2023Article
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- Computational analyses of mechanism of action (MoA): data, methods and integration.RSC chemical biology · 2022Review
- Probabilistic Random Forest improves bioactivity predictions close to the classification threshold by taking into account experimental uncertainty.Journal of cheminformatics · 2021Article
- Exploration of databases and methods supporting drug repurposing: a comprehensive survey.Briefings in bioinformatics · 2021Review
- Leveraging heterogeneous data from GHS toxicity annotations, molecular and protein target descriptors and Tox21 assay readouts to predict and rationalise acute toxicity.Journal of cheminformatics · 2019Article
- In Silico Characterization of Structural Distinctions between Isoforms of Human and Mouse Sphingosine Kinases for Accelerating Drug Discovery.Journal of chemical information and modeling · 2019Article
- Systemic neurotransmitter responses to clinically approved and experimental neuropsychiatric drugs.Nature communications · 2018Article
- Using Machine Learning to Predict Synergistic Antimalarial Compound Combinations With Novel Structures.Frontiers in pharmacology · 2018Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Motivation: In silico approaches often fail to utilize bioactivity data available for orthologous targets due to insufficient evidence highlighting the benefit for such an approach. Deeper investigation into orthologue chemical space and its influence toward expanding compound and target coverage is necessary to improve the confidence in this practice. Results: Here we present analysis of the orthologue chemical space in ChEMBL and PubChem and its impact on target prediction. We highlight the number of conflicting bioactivities between human and orthologues is low and annotations are overall compatible. Chemical space analysis shows orthologues are chemically dissimilar to human with high intra-group similarity, suggesting they could effectively extend the chemical space modelled. Based on these observations, we show the benefit of orthologue inclusion in terms of novel target coverage. We also benchmarked predictive models using a time-series split and also using bioactivities from Chemistry Connect and HTS data available at AstraZeneca, showing that orthologue bioactivity inclusion statistically improved performance. Availability and implementation: Orthologue-based bioactivity prediction and the compound training set are available at www.github.com/lhm30/PIDGINv2. Contact: ab454@cam.ac.uk. Supplementary information: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.