Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water. - Jiali Gao; Kin-Yiu Wong; Dan Thomas Major (J. Comput. Chem., 2007)

Path-integral calculations of heavy atom kinetic isotope effects in condensed phase reactions using higher-order trotter factorizations. - Alexandra Vardi-Kilshtain; Asaf Azuri; Dan Thomas Major (J. Comput. Chem., 2012)

Simulations of remote mutants of dihydrofolate reductase reveal the nature of a network of residues coupled to hydride transfer. - Daniel Roston; Amnon Kohen; Dvir Doron; Dan Thomas Major (J. Comput. Chem., 2014)

Q6: A comprehensive toolkit for empirical valence bond and related free energy calculations. - Paul Bauer; Alexandre Barrozo; Miha Purg; Beat Anton Amrein; Mauricio Esguerra; Philippe Barrie Wilson; Dan Thomas Major; Johan Åqvist; Shina Caroline Lynn Kamerlin (SoftwareX, 2018)

Benchmarking the Ability of Common Docking Programs to Correctly Reproduce and Score Binding Modes in SARS-CoV-2 Protease Mpro. - Shani Zev; Keren Raz; Renana Schwartz; Reem Tarabeh; Prashant Kumar Gupta; Dan T. Major (J. Chem. Inf. Model., 2021)

Utilizing Perturbation of Atoms' Positions for Equivariant Pre-Training in 3D Molecular Analysis. - Tal Kiani; Avi Caciularu; Shani Zev; Dan Thomas Major; Jacob Goldberger (MLSP, 2023)

Template-Based Docking Using Automated Maximum Common Substructure Identification with EnzyDock: Mechanistic and Inhibitor Docking. - Renana Schwartz; Amit Hadar-Volk; Kwangho Nam; Dan T. Major (J. Chem. Inf. Model., 2025)