All posts by Tyler Hughes

Blog, Publication

A Computational Approach to Structural Alerts: Furans, Phenols, Nitroaromatics, and Thiophenes

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A Computational Approach to Structural Alerts: Furans, Phenols, Nitroaromatics, and Thiophenes  Dang, N. L., Hughes, T. B., Miller, G. P., and Swamidass, S. J. (2017). Chemical Research in Toxicology, DOI: 10.1021/acs.chemrestox.6b00336   Abstract: Structural alerts are commonly used in drug discovery to identify molecules likely to form reactive metabolites, and … Continue Reading ››
Blog, Publication

Deep Learning to Predict the Formation of Quinone Species in Drug Metabolism

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Deep Learning to Predict the Formation of Quinone Species in Drug Metabolism

Hughes, T. B. and Swamidass, S. J. (2017). Chemical Research in Toxicology, 30(2), 642–656. TOC   Abstract: Many adverse drug reactions are thought to be caused by electrophilically reactive drug metabolites that conjugate to nucleophilic sites within DNA and proteins,causing cancer … Continue Reading ››
Publication

Update: Modeling Epoxidation of Drug-like Molecules with a Deep Machine Learning Network

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This is a minor update to figure 10 in a recently published paper: Original Paper. The revised figure displays both the RMSE between each method and perfectly scaled prediction, and the R2 values for the Pearson correlation of the best-file line for that method. As measured by RMSE, the three methods have the same relative value as in … Continue Reading ››
Publication

Modeling Epoxidation of Drug-like Molecules with a Deep Machine Learning Network

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Citation: Modeling Epoxidation of Drug-like Molecules with a Deep Machine Learning Network. Tyler B. Hughes, Grover P. Miller, and S. Joshua Swamidass.  ACS Central Science. DOI: 10.1021/acscentsci.5b00131 Abstract:  epox2 Drug toxicity is frequently caused by electrophilic reactive metabolites that covalently bind to proteins. Epoxides comprise … Continue Reading ››
Publication

Combined Analysis of Phenotypic and Target-Based Screening in Assay Networks

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Citation: Swamidass, S. J., Schillebeeckx, C. N., Matlock, M., Hurle, M. R., & Agarwal, P. (2014). Combined Analysis of Phenotypic and Target-Based Screening in Assay Networks. Journal of biomolecular screening, 1087057114523068. Abstract: Small-molecule screens are an integral part of drug discovery. Public domain data in PubChem alone represent more than 158 million measurements, 1.2 million molecules, and 4300 assays. … Continue Reading ››