Web application for studying the free energy of binding and protonation states of protein-ligand complexes based on HINT. - Alexander S. Bayden; Micaela Fornabaio; J. Neel Scarsdale; Glen E. Kellogg (J. Comput. Aided Mol. Des., 2009)

Evaluating Free Energies of Binding and Conservation of Crystallographic Waters Using SZMAP. - Alexander S. Bayden; Demetri T. Moustakas; Diane Joseph-McCarthy; Michelle L. Lamb (J. Chem. Inf. Model., 2015)

PeptideNavigator: An interactive tool for exploring large and complex data sets generated during peptide-based drug design projects. - Kyle I. Diller; Alexander S. Bayden; Joseph Audie; David J. Diller (Comput. Biol. Medicine, 2018)