Jonathan D. Jou

Publication Activity (10 Years)

Years Active: 2015-2020
Publications (10 Years): 10

Top Topics

Sparse Approximations

Protein Structure Alignment

Energy Landscape

Top Venues

J. Comput. Biol.

PLoS Comput. Biol.

J. Comput. Chem.

Publications

Jonathan D. Jou, Graham T. Holt, Anna U. Lowegard, Bruce Randall Donald
Minimization-Aware Recursive K*: A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape. J. Comput. Biol. 27 (4) (2020)
Anna U. Lowegard, Marcel S. Frenkel, Graham T. Holt, Jonathan D. Jou, Adegoke Ojewole, Bruce Randall Donald
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. PLoS Comput. Biol. 16 (6) (2020)
Jonathan D. Jou, Graham T. Holt, Anna U. Lowegard, Bruce Randall Donald
Minimization-Aware Recursive K^* K ∗ ( MARK^* MARK ∗ ): A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape. RECOMB (2019)
Adegoke Ojewole, Jonathan D. Jou, Vance G. Fowler, Bruce Randall Donald
A Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize Stability and Binding Affinity Over Large Sequence Spaces. J. Comput. Biol. 25 (7) (2018)
Mark A. Hallen, Jeffrey W. Martin, Adegoke Ojewole, Jonathan D. Jou, Anna U. Lowegard, Marcel S. Frenkel, Pablo Gainza, Hunter M. Nisonoff, Aditya Mukund, Siyu Wang, Graham T. Holt, David Zhou, Elizabeth Dowd, Bruce Randall Donald
OSPREY 3.0: Open-source protein redesign for you, with powerful new features. J. Comput. Chem. 39 (30) (2018)
Adegoke Ojewole, Jonathan D. Jou, Vance G. Fowler, Bruce Randall Donald
): A Provable and Efficient Ensemble-Based Algorithm to Optimize Stability and Binding Affinity over Large Sequence Spaces. RECOMB (2017)
Mark A. Hallen, Jonathan D. Jou, Bruce Randall Donald
LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid Rotamer-Like Efficiency. J. Comput. Biol. 24 (6) (2017)
Swati Jain, Jonathan D. Jou, Ivelin S. Georgiev, Bruce Randall Donald
A critical analysis of computational protein design with sparse residue interaction graphs. PLoS Comput. Biol. 13 (3) (2017)
Mark A. Hallen, Jonathan D. Jou, Bruce Randall Donald
LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid-rotamer-like Efficiency. RECOMB (2016)
Jonathan D. Jou, Swati Jain, Ivelin Georgiev, Bruce Randall Donald
BWM*: A Novel, Provable, Ensemble-based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design. J. Comput. Biol. 23 (6) (2016)
Jonathan D. Jou, Swati Jain, Ivelin Georgiev, Bruce Randall Donald
BWM*: A Novel, Provable, Ensemble-Based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design. RECOMB (2015)