Epik: a software program for pK a prediction and protonation state generation for drug-like molecules. - John C. Shelley; Anuradha Cholleti; Leah L. Frye; Jeremy R. Greenwood; Mathew R. Timlin; Makoto Uchimaya (J. Comput. Aided Mol. Des., 2007)

Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution. - Jeremy R. Greenwood; David Calkins; Arron P. Sullivan; John C. Shelley (J. Comput. Aided Mol. Des., 2010)

ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers. - K. Shawn Watts; Pranav Dalal; Robert B. Murphy; Woody Sherman; Richard A. Friesner; John C. Shelley (J. Chem. Inf. Model., 2010)

Comments on the Article "Evaluation of pKa Estimation Methods on 211 Druglike Compounds". - John C. Shelley; David Calkins; Arron P. Sullivan (J. Chem. Inf. Model., 2011)

Macrocycle Conformational Sampling with MacroModel. - K. Shawn Watts; Pranav Dalal; Andrew J. Tebben; Daniel L. Cheney; John C. Shelley (J. Chem. Inf. Model., 2014)