• Book: Combined Quantum Mechanical and Molecular Mechanical methods (American Chemical Society ACS Symposium Series) 1997.  ISBN-10: 0841235902).

• Humkey, R. N., Purvis, G. D., Thompson, M. A., and Nigel Richards.  “Enhancing the PMF Scoring Function for Molecular Docking and Virtual Screening”    J. Med. Chem, 2005.

•Feller, D.; Thompson, M. A.; and Rick A. Kendall "A Theoretical Case Study of Substituent Effects and Microsolvation on the Binding Specificity of Crown Ethers" J. Phys. Chem. A 1997, 101, 7292-7298.

•Thompson, M. A. "QM/MMpol: A Consistent Model for Solute/Solvent Polarization. Application to the Aqueous Solvation and Spectroscopy of Formaldehyde, Acetaldehyde, and Acetone" J. Phys. Chem. 1996, 100, 14492-14507.

•Thompson, Mark A. "Molecular Dynamics Study of Li and Still's New Rigidified 18-Crown-6 Derivative Using a    QM/MM Method" Int. J. Quantum Chemistry, 1996, 60, 1133-1141.

•Thompson, Mark A. "Studies of Molecular Recognition Using QM/MM Methods. The Potential of Mean Force for the Association of K+ with 1,2-Dimethoxyethane in Aqueous Solution" Proceedings from the 34th Hanford Symposium on the Environment 1996.

•Brooks, B. R.; Field, M. J.; Gao, J.; and Mark A. Thompson "Hybrid Quantum and Classical Mechanical Methods for Studying Biopolymers in Solution" in Pacific Symposium on Biocomputing Eds. L. Hunter and T. E. Klein. 1996. World Scientific, New Jersey.

•Thompson, Mark A. " A QM/MM Molecular Dynamics Study of the Potential of Mean Force for the Association of   K+ with Dimethylether" in Aqueous Solution" J. Am. Chem. Soc., 1995, 117, 11341-11344.

•Thompson, Mark A. and Gregory K. Schenter. "Excited States of the Bacteriochlorophyll b Dimer of Rhodopseudomonas viridis: A QM/MM Study of the Photosynthetic Reaction Center That Includes MM Polarization" J. Phys. Chem. 1995, 99, 6374-6386.