ALADDIN: An integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure searching of three-dimensional molecular structures. - John H. Van Drie; David Weininger; Yvonne C. Martin (J. Comput. Aided Mol. Des., 1989)

An inequality for 3D database searching and its use in evaluating the treatment of conformational flexibility. - John H. Van Drie (J. Comput. Aided Mol. Des., 1996)

Strategies for the determination of pharmacophoric 3D database queries. - John H. Van Drie (J. Comput. Aided Mol. Des., 1997)

"Shrink-Wrap" Surfaces: A New Method for Incorporating Shape into Pharmacophoric 3D Database Searching. - John H. Van Drie (J. Chem. Inf. Comput. Sci., 1997)

Computer-aided drug design: the next 20 years. - John H. Van Drie (J. Comput. Aided Mol. Des., 2007)

Structure-Activity Landscape Index: Identifying and Quantifying Activity Cliffs. - Rajarshi Guha; John H. Van Drie (J. Chem. Inf. Model., 2008)

Assessing How Well a Modeling Protocol Captures a Structure-Activity Landscape. - Rajarshi Guha; John H. Van Drie (J. Chem. Inf. Model., 2008)

FOCUS - Development of a Global Communication and Modeling Platform for Applied and Computational Medicinal Chemists. - Nikolaus Stiefl; Peter Gedeck; Donovan Chin; Peter Hunt; Mika K. Lindvall; Katrin Spiegel; Clayton Springer; Scott Biller; Christoph L. Buenemann; Takanori Kanazawa; Mitsunori Kato; Richard A. Lewis; et al. (J. Chem. Inf. Model., 2015)

Hit diffusion: limitations to drug discovery and structure-based design. - John H. Van Drie (J. Comput. Aided Mol. Des., 2022)