Bekar-Cesaretli, A., Vats, S., Whitty, A., Kozakov, D., Joseph-Mccarthy, D., Vajda, S. (2025) Impact of Protein Conformational Diversity on Structure-Based Prediction of Druggability. J. Chem Inf. Model.
Khan, O., Jones, G., Kozakov, D., Beglov, D., Joseph-McCarthy, D., Vajda, S. (2025) E-FTMap: A Protein Structure Based Pharmacophore Identification Server for Guiding Fragment Expansion. J. Mol. Biol., 168956.
Yang, J., Walker, K.C., Bekar-Cesaretli, A.A., Hao, B., Bhadelia, N., Joseph-McCarthy, D., Paschalidis, I.C. (2024) Automating biomedical literature review for rapid drug discovery: Leveraging GPT-4 to expedite pandemic response. Int. J. Med. Inform., 189, 105500.
Khan, O., Jones, G., Lazou, M., Joseph-McCarthy, D., Kozakov, D., Vajda, S. (2024) Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites. J. Chem. Inf. Model., 64, 2084.
Li, R., Wilderotter, S., Stoddard, M., Van Egeren, D., Chakravarty, A., Joseph-McCarthy, D. (2024) Computational identification of antibody-binding epitopes from mimotope datasets. Frontiers in Bioinformatics, 4, 1295972.
Bekar-Cesaretli, A., Khan, O., Nguyen, T., Kozakov, D., Joseph-Mccarthy, D., Vajda, S. (2024) Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2, J. Chem. Inf. Model., 64, 960.
Lazou, M., Hutton, J.R., Chakravarty, A., Joseph-McCarthy, D. (2024) Identification of a druggable site on GRP78 at the GRP78-SARS-CoV-2 interface and virtual screening of compounds to disrupt that interface, J. Comp. Aided Mol. Design, 38, 6.
Akash, M.M.H, Lao, Y., Balivada, P.A., Ato, P., Ka, N.K., Mituniewicz, A., Silfen, Z., Suman, J.D., Chakravarty, A., Joseph-McCarthy, D., Basu, S. (2023) On a model-based approach to improve intranasal spray targeting for respiratory viral infections, Front. Drug Deliv., 3, 1164671.
Walker, K.C., Shwarts, M., Demidkin, S., Chakravarty, A., Joseph-McCarthy, D. (2023) Machine learning for the identification of respiratory viral attachment machinery from sequences data, PloS One, 18, e0281642.
Stoddard, M., Novokhodko, A., Sarkar, S., Van Egeren, D., White, L.F., Hochberg, N. S., Rogers, M. S., Zetter, B., Joseph-McCarthy, D. & Chakravarty, A. (2022) Endemicity is not a victory: the unmitigated downside risks of widespread SARS-CoV-2 transmission, COVID 2, 1689.
Basu, S., Akash, M. M. H., Hochberg, N. S., Senior, B. A., Joseph-McCarthy, D., & Chakravarty, A. (2022) From SARS-CoV-2 infection to COVID-19 morbidity: an in silico projection of virion flow rates to the lower airway via nasopharyngeal fluid boluses, Rhinology Online.
Van Egeren, D., Stoddard, M., Novokhodko, A., Rogers, M. S., Joseph-McCarthy, D., Zetter, B., & Chakravarty, A. (2021) Rapid relaxation of pandemic restrictions after vaccine rollout favors growth of SARS-CoV-2 variants: A model-based analysis, PloS One, 16, e0258997.
Van Egeren, D., Novokhodko, A., Stoddard, M., Tran, U., Zetter, B., Rogers, M. S., Joseph-McCarthy, D. & Chakravarty, A. (2021) Controlling long-term SARS-CoV-2 infections can slow viral evolution and reduce the risk of treatment failure, Scientific Reports, 11, 1.
Van Egeren, D., Novokhodko, A., Stoddard, M., Tran, U., Zetter, B., Rogers, M., Pentelute, B.L., Carlson, J.M., Joseph-McCarthy, D. & Chakravarty, A. (2021) Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein, PloS One, 16, e0250780.
Basu, S., Hochberg, N. S., Senior, B. A., Joseph-McCarthy, D., & Chakravarty, A. (2021) Computational projection of virion transmission rates to the lower airway from the initial SARS-CoV-2 infection at the Nasopharynx, Journal of Aerosol Medicine and Pulmonary Drug Delivery, A8-A9.
Koeva, M., Gutu, A.D., Hebert, W, Wager, J.D., Yonker, L.M., O'Toole, G.A., Ausubel, F.M., Moskowitz, SM, Joseph-McCarthy D. (2017) An Antipersister Strategy for Treatment of Chronic Pseudomonas aeruginosa Infections, Antimicrob Agents Chemother., 61, e00987-17.
Bayden, A.S., Moustakas, D.T., Joseph-McCarthy, D., Lamb, M.L. (2015) Evaluating Free Energies of Binding and Conservation of Crystallographic Waters Using SZMAP, J. Chem. Inf. Model., 55, 1552-65.
Campbell, A.J., Lamb, M.L., Joseph-McCarthy, D. (2014) Ensemble-Based Docking Using Biased Molecular Dynamics, J. Chem. Inf. Model., 54, 2127.
Joseph-McCarthy, D., Campbell, A.J., Kern, G., Moustakas, D. (2014) Fragment-Based Lead Discovery and Design, J. Chem. Inf. Model., 54, 693-704.
Martínez-Botella, G., Breen, J.N., Duffy, J.E., Dumas, J., Geng, B., Gowers, I.K., Green, O.M., Guler, S., Hentemann, M.F., Hernandez-Juan, F.A., Joseph-McCarthy, D., Kawatkar, S., Larsen, N.A., Lazari, O., Loch, J.T., Macritchie, J.A., McKenzie, A.R., Newman, J.V., Olivier, N.B., Otterson, L.G., Owens, A.P., Read, J., Sheppard, D.W., Keating, T.A. (2012) Discovery of selective and potent inhibitors of gram-positive bacterial thymidylate kinase (TMK), J. Med. Chem., 55, 10010-21.