Prediction of Mutational Tolerance in HIV-1 Protease and Reverse Transcriptase Using Flexible Backbone Protein Design. - Elisabeth Humphris-Narayanan; Eyal Akiva; Rocco Varela; Shane Ó Conchúir; Tanja Kortemme (PLoS Comput. Biol., 2012)

A structure-guided approach for protein pocket modeling and affinity prediction. - Rocco Varela; Ann E. Cleves; Russell Spitzer; Ajay N. Jain (J. Comput. Aided Mol. Des., 2013)

Physical Binding Site Modeling for Quantitative Prediction of Biological Activities. - Lawrence Rocco Varela (2013)

Surflex-QMOD: physically meaningful QSAR. - Alexander Steudle; Rocco Varela; Ajay N. Jain (J. Cheminformatics, 2014)