The Joseph-McCarthy Group is focused on understanding receptor-ligand interactions at a detailed molecular level and translating those insights into the development of novel computational approaches to accelerate drug design.
Areas of particular interest involve developing new methods for
Target identification and evaluation
Druggability assessment for proteins (structures and models) for targets of therapeutic interest including cryptic sites
The study of beyond rule of five targets including protein-protein interfaces
AI-based prediction of antibody-antigen binding
Generating realistic ensembles of protein conformations for use in druggability assessment and molecular docking
This research necessitates the development and use of large language models, neural network models, binding site hot spot mapping/fragment positioning techniques, and molecular dynamics simulations, and other bioinformatics tools. A recent application of related approaches was to the development of pandemic prevention and mitigation strategies, as part of an NSF Predictive Intelligence for Pandemic Preparedness grant (NSF-2200052) and a Merck Research SEEDS grant.