GenStar: A method for de novo drug design. - Sergio H. Rotstein; Mark A. Murcko (J. Comput. Aided Mol. Des., 1993)

ArQiologist: An Integrated Decision Support Tool for Lead Optimization. - Atipat Rojnuckarin; Daniel A. Gschwend; Sergio H. Rotstein; David S. Hartsough (J. Chem. Inf. Model., 2005)

HELM: A Hierarchical Notation Language for Complex Biomolecule Structure Representation. - Tianhong Zhang; Hongli Li; Hualin Xi; Robert V. Stanton; Sergio H. Rotstein (J. Chem. Inf. Model., 2012)

HELM Software for Biopolymers. - Edward J. Milton; Tianhong Zhang; Claire Bellamy; Gregg Alan Swayze; Christopher Hart; Markus Weisser; Sabrina Hecht; Sergio H. Rotstein (J. Chem. Inf. Model., 2017)