Art and technology: very large scale integration. - Tom Meyer; Sally Rosenthal; Stephen R. Johnson; Mary Lou Jepsen; Douglas Davis (SIGGRAPH, 1994)

In silico ADME/Tox: why models fail. - Terry R. Stouch; James R. Kenyon; Stephen R. Johnson; Xue-Qing Chen; Arthur M. Doweyko; Yi Li (J. Comput. Aided Mol. Des., 2003)

A Novel Method to Simulate the Hydrophobic Effect and Its Application to the Ranking of Host/Guest Complexes. - Arthur M. Doweyko; Stephen R. Johnson (J. Chem. Inf. Model., 2006)

The Trouble with QSAR (or How I Learned To Stop Worrying and Embrace Fallacy). - Stephen R. Johnson (J. Chem. Inf. Model., 2008)

PathCase-MAW: An Online Metabolic Network Analysis Workbench. - A. Ercüment Çiçek; Xinjian Qi; Ali Cakmak 001; Stephen R. Johnson; Xu Han; Sami Alshalwi; Gultekin Özsoyoglu (BCB, 2013)

iPathCaseKEGG: An iPad interface for KEGG metabolic pathways. - Stephen R. Johnson; Xinjian Qi; A. Ercüment Çiçek; Gultekin Özsoyoglu (Health Inf. Sci. Syst., 2013)

3D Matched Pairs: Integrating Ligand- and Structure-Based Knowledge for Ligand Design and Receptor Annotation. - Shana L. Posy; Brian L. Claus; Matt E. Pokross; Stephen R. Johnson (J. Chem. Inf. Model., 2013)

An online system for metabolic network analysis. - Abdullah Ercument Cicek; Xinjian Qi; Ali Cakmak 001; Stephen R. Johnson; Xu Han; Sami Alshalwi; Zehra Meral Özsoyoglu; Gultekin Özsoyoglu (Database J. Biol. Databases Curation, 2014)

Electrostatic-field and surface-shape similarity for virtual screening and pose prediction. - Ann E. Cleves; Stephen R. Johnson; Ajay N. Jain (J. Comput. Aided Mol. Des., 2019)

Synergy and Complementarity between Focused Machine Learning and Physics-Based Simulation in Affinity Prediction. - Ann E. Cleves; Stephen R. Johnson; Ajay N. Jain (J. Chem. Inf. Model., 2021)

MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics. - Alexander C. Brueckner; Benjamin Shields; Palani Kirubakaran; Alexander Suponya; Manoranjan Panda; Shana L. Posy; Stephen R. Johnson; Sirish Kaushik Lakkaraju (J. Comput. Aided Mol. Des., 2024)