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High-Throughput Screening (HTS) is a pharmaceutical industry standard for the discovery of drugs with new or improved properties that is now increasingly being implemented in academic institutions as well. Miniaturization of bioassays, availability of  structurally diverse compounds, and developments in sensitive and rapid detection instrumentation permit thousands of compounds to be assayed for a desired function in vitro, in cellulo and even in vivo. When integrated with modeling and/or cheminformatics-based virtual pre-screens, the number of compounds that needs to be evaluated could be reduced significantly by in silico methods to make screening a reasonable and, yet, powerful option for chemical probe/drug discovery in an academic setting, where resources could be limited. Rather than focusing solely on hits, a range of cheminformatic tools (similarity co-clustering, R-group analysis, QSAR, descriptor bias analysis, etc.) can be used to reveal structure-activity relationships, descriptor trends, and models to guide the next iteration of focused screens and/or medicinal chemistry elaborations toward a viable candidate for probing cellular events or drug discovery.