Morgan C. Thomas, PhD

Morgan C. Thomas, PhD

AI/ML for Drug Discovery

Publications

You can also find my articles on my Google Scholar profile.
  1. Thomas, M., Bou, A., & De Fabritiis, G. (2025). Test-Time Training Scaling for Chemical Exploration in Drug Design. ArXiv Preprint ArXiv:2501.19153.
  2. Thomas, M., Bou, A., & De Fabritiis, G. (2025). REINFORCE-ING Chemical Language Models in Drug Design. ArXiv Preprint ArXiv:2501.15971.
  3. Thomas, M., O’Boyle, N. M., Bender, A., & De Graaf, C. (2024). MolScore: a scoring, evaluation and benchmarking framework for generative models in de novo drug design. Journal of Cheminformatics, 16(1), 64.
  4. Bou, A., Thomas, M., Dittert, S., Navarro, C., Majewski, M., Wang, Y., Patel, S., Tresadern, G., Ahmad, M., Moens, V., & others. (2024). ACEGEN: Reinforcement learning of generative chemical agents for drug discovery. Journal of Chemical Information and Modeling, 64(15), 5900–5911.
  5. Peter, S., Siragusa, L., Thomas, M., Palomba, T., Cross, S., O’Boyle, N. M., Bajusz, D., Ferenczy, G. G., Keserű, G. M., Bottegoni, G., & others. (2024). Comparative Study of Allosteric GPCR Binding Sites and Their Ligandability Potential. Journal of Chemical Information and Modeling, 64(21), 8176–8192.
  6. Thomas, M., Ahmad, M., Tresadern, G., & De Fabritiis, G. (2024). PromptSMILES: prompting for scaffold decoration and fragment linking in chemical language models. Journal of Cheminformatics, 16(1), 77.
  7. Thomas, M., Matricon, P. G., Gillespie, R. J., Napiórkowska, M., Neale, H., Mason, J. S., Brown, J., Fieldhouse, C., Swain, N. A., Geng, T., & others. (2024). Modern hit-finding with structure-guided de novo design: identification of novel nanomolar adenosine A2A receptor ligands using reinforcement learning.
  8. Thomas, M., Bender, A., & de Graaf, C. (2023). Integrating structure-based approaches in generative molecular design. Current Opinion in Structural Biology, 79, 102559.
  9. Handa, K., Thomas, M. C., Kageyama, M., Iijima, T., & Bender, A. (2023). On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data. Journal of Cheminformatics, 15(1), 112.
  10. Staniszewska, A. D., Armenia, J., King, M., Michaloglou, C., Reddy, A., Singh, M., San Martin, M., Prickett, L., Wilson, Z., Proia, T., & others. (2022). PARP inhibition is a modulator of anti-tumor immune response in BRCA-deficient tumors. Oncoimmunology, 11(1), 2083755.
  11. Thomas, M., O’Boyle, N. M., Bender, A., & De Graaf, C. (2022). Augmented Hill-Climb increases reinforcement learning efficiency for language-based de novo molecule generation. Journal of Cheminformatics, 14(1), 68.
  12. Thomas, M., O’Boyle, N. M., Bender, A., & De Graaf, C. (2022). Re-evaluating sample efficiency in de novo molecule generation. ArXiv Preprint ArXiv:2212.01385.
  13. Thomas, M., Smith, R. T., O’Boyle, N. M., de Graaf, C., & Bender, A. (2021). Comparison of structure-and ligand-based scoring functions for deep generative models: a GPCR case study. Journal of Cheminformatics, 13(1), 39.
  14. Thomas, M., Boardman, A., Garcia-Ortegon, M., Yang, H., de Graaf, C., & Bender, A. (2021). Applications of artificial intelligence in drug design: opportunities and challenges. Artificial Intelligence in Drug Design, 1–59.
  15. Raubo, P., Carbajo, R. J., McCoull, W., Raubo, J., & Thomas, M. (2021). Diversity-orientated synthesis of macrocyclic heterocycles using a double SN Ar approach. Organic & Biomolecular Chemistry, 19(28), 6274–6290.
  16. McAulay, K., Hoyt, E. A., Thomas, M., Schimpl, M., Bodnarchuk, M. S., Lewis, H. J., Barratt, D., Bhavsar, D., Robinson, D. M., Deery, M. J., & others. (2020). Alkynyl benzoxazines and dihydroquinazolines as cysteine targeting covalent warheads and their application in identification of selective irreversible kinase inhibitors. Journal of the American Chemical Society, 142(23), 10358–10372.
  17. Burton, M. J., Cresser-Brown, J., Thomas, M., Portolano, N., Basran, J., Freeman, S. L., Kwon, H., Bottrill, A. R., Llansola-Portoles, M. J., Pascal, A. A., & others. (2020). Discovery of a heme-binding domain in a neuronal voltage-gated potassium channel. Journal of Biological Chemistry, 295(38), 13277–13286.