Y. Khalak (2019). Model development: reproducing properties of water. Technische Universiteit Eindhoven. ISBN: 978-90-386-4701-2.

Y. Khalak, G. Tresadern, D. F. Hahn, B. L. de Groot, & V. Gapsys (2022). Chemical space exploration with active learning and alchemical free energies. Journal of Chemical Theory and Computation, 18(10), 6259-6270. doi:10.1021/acs.jctc.2c00752

Y. Khalak, G. Tresadern, M. Aldeghi, H. M. Baumann, D. L. Mobley, & B. L. de Groot, V. Gapsys (2021). Alchemical absolute protein–ligand binding free energies for drug design. Chemical Science, 12(41), 13958-13971. doi:10.1039/D1SC03472C

V. Gapsys, A. Yildirim, M. Aldeghi, Y. Khalak, D. van der Spoel, & B. L. de Groot (2021). Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches. Communications Chemistry, 4(1), 1-13. doi:10.1038/s42004-021-00498-y

Y. Khalak, G. Tresadern, B. L. de Groot, V. Gapsys (2021). Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software. Journal of Computer-Aided Molecular Design, 35(1), 49-61. doi:10.1007/s10822-020-00359-1

Y. Khalak, B. Baumeier, and M. Karttunen (2018). Improved general-purpose five-point model for water: TIP5P/2018. The Journal of Chemical Physics, 149(22), 224507. doi:10.1063/1.5070137

Y. Khalak (2023). Learning to Bind: Active Learning for In Silico Ligand Optimization.