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 ››
This week (December 4-5, 2012), I am honored to chair and present at the World Drug Repositioning Conference in Washington DC. This conference brings together several key industry groups to share insight into how they are discovering new uses for drugs in their pipelines. The second day of the conference, I will be presenting on technology developed … Continue Reading ››