* Using Quantum Mechanical Approaches to Study Biological Systems; K. M. Merz, Jr. Acc. Chem. Res. 2014 47, 2804–2811.
* Open-source multi-GPU-accelerated QM/MM simulations with AMBER and QUICK; V. Cruzeiro; M. Manathunga; K. M. Merz, Jr.; A. W. Götz J. Chem Inf. Model 2021, 61, 2109–2115.
* A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids and Organic Molecules; W. D. Cornell; P. Cieplak; C. I. Bayly; I. R. Gould; K. M. Merz, Jr. D. M. Ferguson; D. C. Spellmeyer; T. Fox; J. W. Cladwell; P. A. Kollman J. Am. Chem. Soc. 1995, 117, 5179-5197.
* Metal Ion Modeling Using Classical Mechanics; P. Li; K. M. Merz, Jr. Chemical Reviews, 2017, 117, 1564–1686.
* Atomic Charges Derived from Semiempirical Methods; B. H. Besler, K. M. Merz, Jr., and P. A. Kollman J. Comput. Chem.1990, 11, 431-439.
* Free Energy Perturbation Simulations of the Inhibition of Thermolysin: Prediction of the Free Energy of Binding of a New Inhibitor; K. M. Merz Jr. and P. A. Kollman J. Am. Chem. Soc. 1989, 111, 5649-5658.
* The Amber Biomolecular Simulation Program; D. A. Case; T. E. Cheatham, III; T. Darden; H. Gohlke; R. Luo; K. M. Merz, Jr.; A. Onufriev; C. Simmerling; B. Wang; R. J. Woods J. Comput. Chem. 2005, 26, 1668-1688.
* Harnessing the Power of Multi-GPU Acceleration into the Quantum Interaction Computational Kernel Program; M. Manathunga; C. Jin; V. Cruzeiro; Y. Miao; D. Mu; K. Arumugam; K. Keipert; H. M. Aktulga; K. M. Merz, Jr.; A. Goetz J. Chem. Theory Comput. 2021.