Assessing search strategies for flexible docking. - Michal Vieth; Jonathan D. Hirst; Brian N. Dominy; Heidi Daigler; Charles L. Brooks III (J. Comput. Chem., 1998)

Identifying native-like protein structures using physics-based potentials. - Brian N. Dominy; Charles L. Brooks III (J. Comput. Chem., 2002)

Comparison of solvation-effect methods for the simulation of peptide interactions with a hydrophobic surface. - Yu Sun; Brian N. Dominy; Robert A. Latour (J. Comput. Chem., 2007)

Analyzing the robustness of the MM/PBSA free energy calculation method: Application to DNA conformational transitions. - Allyn R. Brice; Brian N. Dominy (J. Comput. Chem., 2011)

Effects from metal ion in tumor endothelial marker 8 and anthrax protective antigen: BioLayer Interferometry experiment and molecular dynamics simulation study. - Zhe Jia; Christine Ackroyd; Tingting Han; Vibhor Agrawal; Yinling Liu; Kenneth Christensen; Brian N. Dominy (J. Comput. Chem., 2017)