Dead-end elimination for multistate protein design. - Chen Yanover; Menachem Fromer; Julia M. Shifman (J. Comput. Chem., 2007)

Tradeoff Between Stability and Multispecificity in the Design of Promiscuous Proteins. - Menachem Fromer; Julia M. Shifman (PLoS Comput. Biol., 2009)

Optimizing energy functions for protein-protein interface design. - Oz Sharabi; Chen Yanover; Ayelet Dekel; Julia M. Shifman (J. Comput. Chem., 2011)

Cold Spot SCANNER: Colab Notebook for predicting cold spots in protein-protein interfaces. - Sagara N. S. Gurusinghe; Julia M. Shifman (BMC Bioinform., 2024)