ForceFit: A code to fit classical force fields to quantum mechanical potential energy surfaces. - Benjamin Waldher; Jadwiga Kuta; Samuel Chen; Neil J. Henson; Aurora E. Clark (J. Comput. Chem., 2010)

MoleculaRnetworks: An integrated graph theoretic and data mining tool to explore solvent organization in molecular simulation. - Barbara Logan Mooney; L. René Corrales; Aurora E. Clark (J. Comput. Chem., 2012)

ChemNetworks: A complex network analysis tool for chemical systems. - Abdullah Ozkanlar; Aurora E. Clark (J. Comput. Chem., 2014)

DELTA-Topology: A Science Gateway for Experimental and Computational Chemical Data Analysis using Topological Models. - Sudhakar Pamidighantam; Eric Coulter; Marcus Christie; Aurora E. Clark (PEARC, 2021)