Optimization of the Lennard-Jones parameters for a combined ab initio quantum mechanical and molecular mechanical potential using the 3-21G basis set. - Marek Freindorf; Jiali Gao (J. Comput. Chem., 1996)

Lennard-Jones parameters for the combined QM/MM method using the B3LYP/6-31G*/AMBER potential. - Marek Freindorf; Yihan Shao; Thomas R. Furlani; Jing Kong (J. Comput. Chem., 2005)

Combined QM/MM Studies of Binding Effect of Cytochrome P450cam to Putidaredoxin. - Marek Freindorf; Yihan Shao; Jing Kong; Thomas R. Furlani (BIOCOMP, 2006)

Large-Scale QM/MM Calculations of Electronic Excitations in Yellow Protein: Toward Petascale Level of Protein Calculations. - Marek Freindorf; Matthew D. Jones; Yihan Shao; Jing Kong; Thomas R. Furlani (BIBE, 2007)

A Critical Evaluation of Vibrational Stark Effect (VSE) Probes with the Local Vibrational Mode Theory. - Niraj Verma; Yunwen Tao; Wenli Zou; Xia Chen; Xin Chen; Marek Freindorf; Elfi Kraka (Sensors, 2020)

CO bonding in hexa- and pentacoordinate carboxy-neuroglobin: A quantum mechanics/molecular mechanics and local vibrational mode study. - Marek Freindorf; Alexis Antoinette Ann Delgado; Elfi Kraka (J. Comput. Chem., 2022)

Iron-histidine bonding in bishistidyl hemoproteins-A local vibrational mode study. - Marek Freindorf; Juliana J. Antonio; Elfi Kraka (J. Comput. Chem., 2024)

A Closer Look at the FeS Heme Bonds in Azotobacter vinelandii Bacterioferritin: QM/MM and Local Mode Analysis. - Marek Freindorf; Elfi Kraka (J. Comput. Chem., 2025)