Proof of principle for epitope-focused vaccine design. - Bruno E. Correia; John T. Bates; Rebecca J. Loomis; Gretchen Baneyx; Chris Carrico; Joseph G. Jardine; Peter Rupert; Colin E. Correnti; Oleksandr Kalyuzhniy; Vinayak Vittal; Mary J. Connell; Eric Stevens; et al. (Nat., 2014)

: Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial. - Paul Thatcher Edlefsen; Morgane Rolland; Tomer Hertz; Sodsai Tovanabutra; Andrew J. Gartland; Allan C. deCamp; Craig A. Magaret; Hasan Ahmed; Raphael Gottardo; Michal Juraska; Connor McCoy; Brendan B. Larsen; et al. (PLoS Comput. Biol., 2015)

Residue-centric modeling and design of saccharide and glycoconjugate structures. - Jason W. Labonte; Jared Adolf-Bryfogle; William R. Schief; Jeffrey J. Gray (J. Comput. Chem., 2017)

RosettaAntibodyDesign (RAbD): A general framework for computational antibody design. - Jared Adolf-Bryfogle; Oleksandr Kalyuzhniy; Michael Kubitz; Brian D. Weitzner; Xiaozhen Hu; Yumiko Adachi; William R. Schief; Roland L. Dunbrack Jr. (PLoS Comput. Biol., 2018)

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)

CoV3D: a database of high resolution coronavirus protein structures. - Ragul Gowthaman; Johnathan D. Guest; Rui Yin 004; Jared Adolf-Bryfogle; William R. Schief; Brian G. Pierce (Nucleic Acids Res., 2021)

Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design. - Jared Adolf-Bryfogle; Jason W. Labonte; John C. Kraft; Maxim Shapovalov; Sebastian Raemisch; Thomas Lütteke; Frank Dimaio; Christopher D. Bahl; Jesper Pallesen; Neil P. King; Jeffrey J. Gray; Daniel W. Kulp; et al. (PLoS Comput. Biol., 2024)