Design of Multi-Specificity in Protein Interfaces. - Elisabeth L. Humphris; Tanja Kortemme (PLoS Comput. Biol., 2007)

SAT-based protein design. - Noah Ollikainen; Ellen Sentovich; Carlos Coelho; Andreas Kuehlmann; Tanja Kortemme (ICCAD, 2009)

A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family. - Gregory D. Friedland; Nils-Alexander Lakomek; Christian Griesinger; Jens Meiler; Tanja Kortemme (PLoS Comput. Biol., 2009)

RosettaBackrub - a web server for flexible backbone protein structure modeling and design. - Florian Lauck; Colin A. Smith; Gregory F. Friedland; Elisabeth L. Humphris; Tanja Kortemme (Nucleic Acids Res., 2010)

Global landscape of HIV-human protein complexes. - Stefanie Jäger; Peter Cimermancic; Natali Gulbahce; Jeffrey R. Johnson; Kathryn E. McGovern; Starlynn C. Clarke; Michael Shales; Gaelle Mercenne; Lars Pache; Kathy Li; Hilda Hernandez; Gwendolyn M. Jang; et al. (Nat., 2012)

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)

Computational Protein Design Quantifies Structural Constraints on Amino Acid Covariation. - Noah Ollikainen; Tanja Kortemme (PLoS Comput. Biol., 2013)

Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity. - Noah Ollikainen; René M. de Jong; Tanja Kortemme (PLoS Comput. Biol., 2015)

Better together: Elements of successful scientific software development in a distributed collaborative community. - Julia Koehler Leman; Brian D. Weitzner; P. Douglas Renfrew; Steven M. Lewis; Rocco Moretti; Andrew M. Watkins; Vikram Khipple Mulligan; Sergey Lyskov; Jared Adolf-Bryfogle; Jason W. Labonte; Justyna Krys; RosettaCommons Consortium; et al. (PLoS Comput. Biol., 2020)

New computational protein design methods for de novo small molecule binding sites. - James E. Lucas; Tanja Kortemme (PLoS Comput. Biol., 2020)

De novo protein fold families expand the designable ligand binding site space. - Xingjie Pan; Tanja Kortemme (PLoS Comput. Biol., 2021)

Advances in the Computational Design of Small-Molecule-Controlled Protein-Based Circuits for Synthetic Biology. - Simon Kretschmer; Tanja Kortemme (Proc. IEEE, 2022)

An integrative approach to protein sequence design through multiobjective optimization. - Lu Hong; Tanja Kortemme (PLoS Comput. Biol., 2024)