BWM*: A Novel, Provable, Ensemble-based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design. - Jonathan D. Jou; Swati Jain; Ivelin Georgiev; Bruce Randall Donald (J. Comput. Biol., 2016)

BBK* (Branch and Bound over K*): A Provable and Efficient Ensemble-Based Algorithm to Optimize Stability and Binding Affinity over Large Sequence Spaces. - Adegoke A. Ojewole; Jonathan D. Jou; Vance G. Fowler; Bruce Randall Donald (RECOMB, 2017)

LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid Rotamer-Like Efficiency. - Mark A. Hallen; Jonathan D. Jou; Bruce Randall Donald (J. Comput. Biol., 2017)

A critical analysis of computational protein design with sparse residue interaction graphs. - Swati Jain; Jonathan D. Jou; Ivelin S. Georgiev; Bruce Randall Donald (PLoS Comput. Biol., 2017)

BBK* (Branch and Bound Over K*): A Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize Stability and Binding Affinity Over Large Sequence Spaces. - Adegoke A. Ojewole; Jonathan D. Jou; Vance G. Fowler; Bruce Randall Donald (J. Comput. Biol., 2018)

OSPREY 3.0: Open-source protein redesign for you, with powerful new features. - Mark A. Hallen; Jeffrey W. Martin; Adegoke A. Ojewole; Jonathan D. Jou; Anna U. Lowegard; Marcel S. Frenkel; Pablo Gainza; Hunter M. Nisonoff; Aditya Mukund; Siyu Wang; Graham T. Holt; David Zhou; et al. (J. Comput. Chem., 2018)

Novel Computational Protein Design Algorithms with Sparse Residue Interaction Graphs, Ensembles, and Mathematical Guarantees, and their Application to Antibody Design. - Jonathan D. Jou (2018)

Minimization-Aware Recursive K^* K ∗ ( MARK^* MARK ∗ ): A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape. - Jonathan D. Jou; Graham T. Holt; Anna U. Lowegard; Bruce Randall Donald (RECOMB, 2019)

Minimization-Aware Recursive K*: A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape. - Jonathan D. Jou; Graham T. Holt; Anna U. Lowegard; Bruce Randall Donald (J. Comput. Biol., 2020)

Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD: KRas protein-protein interface. - Anna U. Lowegard; Marcel S. Frenkel; Graham T. Holt; Jonathan D. Jou; Adegoke A. Ojewole; Bruce Randall Donald (PLoS Comput. Biol., 2020)