The tetracycline: Mg2+ complex: A molecular mechanics force field. - Alexey Aleksandrov; Thomas Simonson (J. Comput. Chem., 2006)

Molecular mechanics models for tetracycline analogs. - Alexey Aleksandrov; Thomas Simonson (J. Comput. Chem., 2009)

A molecular mechanics model for imatinib and imatinib: kinase binding. - Alexey Aleksandrov; Thomas Simonson (J. Comput. Chem., 2010)

Computational modelling elucidates the mechanism of ciliary regulation in health and disease. - Nikolay V. Kotov; Declan G. Bates; Antonina N. Gizatullina; Bulat Gilaziev; Rustem N. Khairullin; Michael Z. Q. Chen; Ignat Drozdov; Yoshinori Umezawa; Christian Hundhausen; Alexey Aleksandrov; Xing-Gang Yan 001; Sarah K. Spurgeon; et al. (BMC Syst. Biol., 2011)

Additive CHARMM force field for naturally occurring modified ribonucleotides. - You Xu; Kenno Vanommeslaeghe; Alexey Aleksandrov; Alexander D. MacKerell Jr.; Lennart Nilsson (J. Comput. Chem., 2016)

Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model. - Alexey Aleksandrov; Fang-Yu Lin; Benoît Roux; Alexander D. MacKerell Jr. (J. Comput. Chem., 2018)

A Molecular Mechanics Model for Flavins. - Alexey Aleksandrov (J. Comput. Chem., 2019)

Parametrization of Force Field Bonded Terms under Structural Inconsistency. - Anastasia Croitoru; Alexey Aleksandrov (J. Chem. Inf. Model., 2022)

Additive CHARMM Force Field for Pterins and Folates. - Elsa Balduzzi; Wenlu Yin; Jean-Christophe Lambry; Hannu Myllykallio; Alexey Aleksandrov (J. Comput. Chem., 2025)