PublicaTions

Lazou, M., Tuchscherer,, F., Vajda, S., Joseph-McCarthy, D. (2026) The Influence of Ligands on AlphaFold3 Prediction of Cryptic Pockets. Commun. Biol., in press. 

Talaei, M., Walker, K.C., Hao, B.,Jolley, E., Jin, Y., Kozakov, D., Misasi, J., Vajda, S., Paschalidis, I. Ch., Joseph-McCarthy, D. (2026) Preferential CDR masking in paired antibody language models improves binding affinity prediction. Commun. AI & Comput., in press.

Maidanik, H., Lazou, M., Bajaj, R., Sarwar, R., Ziaee, O., Vajda, S., Joseph-McCarthy, D. (2026) Assessment of Alphafold Protein Models for Small-Molecule Ligand Docking versus Co-Folding (2026) J. Chem. Inf. Model., 66, 5811.

Khan O, Kankkunen M, Shaker M, Henry Chow, H., Moustakas, N., Allegra-Berger, S., Vajda, S., Joseph-McCarthy, D. (2026) Toward understanding the drivers of antibody-antigen binding. Biophysical J., 0.

Andricioaei, I., et al. (2026) The scientific legacy of Martin Karplus from the perspective of his collaborators. Biophysical J., 0.

H Yu, AA Bekar-Cesaretli, M Lazou, D Kozakov, D Joseph-McCarthy, Vajda, S. (2026) Bias in the AlphaFold3 prediction of ligand-induced domain motion in enzymes. PNAS, 123, e2530709123.

R Ashizawa, et al. (2026) Modeling Protein–Protein and Protein–Ligand Interactions by the ClusPro Team in CASP16.

Proteins, 94, 183.

Ostrovsky, N., Ragatz, A., Wong, J.Y., Joseph-McCarthy, D. (2025) Investigation of Peptide Binding to Fibrin for the Design of Targeted Molecular Imaging Agents. Langmuir, 42, 322.

H Yu, D Joseph-McCarthy, S Vajda. (2025) Improving B-cell epitope prediction. Drug Discov.Today, 30, 104489.

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., 65, 9287.

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.

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.