CoC: a database of universally conserved residues in protein folds. - Jason E. Donald; Isaac A. Hubner; Veronica Rotemberg; Eugene I. Shakhnovich; Leonid A. Mirny (Bioinform., 2005)

Determining functional specificity from protein sequences. - Jason E. Donald; Eugene I. Shakhnovich (Bioinform., 2005)

SDR: a database of predicted specificity-determining residues in proteins. - Jason E. Donald; Eugene I. Shakhnovich (Nucleic Acids Res., 2009)

Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL). - Daniel W. Kulp; Sabareesh Subramaniam; Jason E. Donald; Brett T. Hannigan; Benjamin K. Mueller; Gevorg Grigoryan; Alessandro Senes (J. Comput. Chem., 2012)