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

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 ››

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

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 ››

Sharing Chemical Relationships Does Not Reveal Structures

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 ››

computation at the intersection of medicine, biology and chemistry.