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: Drug toxicity is frequently caused by electrophilic reactive metabolites that covalently bind to proteins. Epoxides comprise … Continue Reading ››
Published online in Bioinformatics in February 2015 Extending P450 Site-of-Metabolism Models with Region-Resolution Data Jed Zaretzki, Michael Browning, Tyler B. Hughes, S. Joshua SwamidassMotivation: Cytochrome P450s are a family of enzymes responsible for the metabolism of approximately 90% of FDA approved drugs. Medicinal chemists often want to know which atoms of a … Continue Reading ››
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 ››
Citation: Matlock, M., & Swamidass, S. J. (2013). Sharing Chemical Relationships Does Not Reveal Structures. Journal of chemical information and modeling, 54(1), 37-48. Abstract: In this study, we propose a new, secure method of sharing useful chemical information from small-molecule libraries, without revealing the structures of the libraries’ molecules. Our method shares the relationship between molecules rather … Continue Reading ››
Web Server: http://swami.wustl.edu/xenosite Citation: Zaretzki, J., Matlock, M., & Swamidass, S. J. (2013). XenoSite: Accurately predicting CYP-mediated sites of metabolism with neural networks. Journal of chemical information and modeling, 53(12), 3373-3383.. Abstract: Understanding how xenobiotic molecules are metabolized is important because it influences the safety, efficacy, and dose of medicines and how they can be modified to improve these … Continue Reading ››
Over the last several months we have published several papers. In the coming weeks, I will be posting abstracts and additional information for each of these papers. In the meantime, here are the citations of those that have hit print.
Managing missing measurements in small-molecule screens. Browning MR, Calhoun BT, Swamidass SJ. J Comput Aided Mol Des. 2013 … Continue Reading ››